nipype.interfaces.freesurfer.utils module

Interfaces to assorted Freesurfer utility programs.

AddXFormToHeader

Link to code

Bases: FSCommand

Wrapped executable: mri_add_xform_to_header.

Just adds specified xform to the volume header.

Danger

Input transform MUST be an absolute path to a DataSink’ed transform or the output will reference a transform in the workflow cache directory!

Examples

>>> from nipype.interfaces.freesurfer import AddXFormToHeader
>>> adder = AddXFormToHeader()
>>> adder.inputs.in_file = 'norm.mgz'
>>> adder.inputs.transform = 'trans.mat'
>>> adder.cmdline
'mri_add_xform_to_header trans.mat norm.mgz output.mgz'

>>> adder.inputs.copy_name = True
>>> adder.cmdline
'mri_add_xform_to_header -c trans.mat norm.mgz output.mgz'
>>> adder.run()   # doctest: +SKIP

References

[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_add_xform_to_header]

in_file : a pathlike object or string representing an existing file
Input volume. Maps to a command-line argument: %s (position: -2).
transform : a pathlike object or string representing a file
Xfm file. Maps to a command-line argument: %s (position: -3).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
copy_name : a boolean
Do not try to load the xfmfile, just copy name. Maps to a command-line argument: -c.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output volume. Maps to a command-line argument: %s (position: -1). (Nipype default value: output.mgz)
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
verbose : a boolean
Be verbose. Maps to a command-line argument: -v.
out_file : a pathlike object or string representing an existing file
Output volume.

Aparc2Aseg

Link to code

Bases: FSCommand

Wrapped executable: mri_aparc2aseg.

Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would. The algorithm is to find each aseg voxel labeled as cortex (3 and 42) and assign it the label of the closest cortical vertex. If the voxel is not in the ribbon (as defined by mri/ lh.ribbon and rh.ribbon), then the voxel is marked as unknown (0). This can be turned off with --noribbon. The cortical parcellation is obtained from subject/label/hemi.aparc.annot which should be based on the curvature.buckner40.filled.desikan_killiany.gcs atlas. The aseg is obtained from subject/mri/aseg.mgz and should be based on the RB40_talairach_2005-07-20.gca atlas. If these atlases are used, then the segmentations can be viewed with tkmedit and the FreeSurferColorLUT.txt color table found in $FREESURFER_HOME. These are the default atlases used by recon-all.

Examples

>>> from nipype.interfaces.freesurfer import Aparc2Aseg
>>> aparc2aseg = Aparc2Aseg()
>>> aparc2aseg.inputs.lh_white = 'lh.pial'
>>> aparc2aseg.inputs.rh_white = 'lh.pial'
>>> aparc2aseg.inputs.lh_pial = 'lh.pial'
>>> aparc2aseg.inputs.rh_pial = 'lh.pial'
>>> aparc2aseg.inputs.lh_ribbon = 'label.mgz'
>>> aparc2aseg.inputs.rh_ribbon = 'label.mgz'
>>> aparc2aseg.inputs.ribbon = 'label.mgz'
>>> aparc2aseg.inputs.lh_annotation = 'lh.pial'
>>> aparc2aseg.inputs.rh_annotation = 'lh.pial'
>>> aparc2aseg.inputs.out_file = 'aparc+aseg.mgz'
>>> aparc2aseg.inputs.label_wm = True
>>> aparc2aseg.inputs.rip_unknown = True
>>> aparc2aseg.cmdline # doctest: +SKIP
'mri_aparc2aseg --labelwm  --o aparc+aseg.mgz --rip-unknown --s subject_id'
lh_annotation : a pathlike object or string representing an existing file
Input file must be <subject_id>/label/lh.aparc.annot.
lh_pial : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/lh.pial.
lh_ribbon : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/lh.ribbon.mgz.
lh_white : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/lh.white.
out_file : a pathlike object or string representing a file
Full path of file to save the output segmentation in. Maps to a command-line argument: --o %s.
rh_annotation : a pathlike object or string representing an existing file
Input file must be <subject_id>/label/rh.aparc.annot.
rh_pial : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/rh.pial.
rh_ribbon : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/rh.ribbon.mgz.
rh_white : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/rh.white.
ribbon : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/ribbon.mgz.
subject_id : a string
Subject being processed. Maps to a command-line argument: --s %s. (Nipype default value: subject_id)
a2009s : a boolean
Using the a2009s atlas. Maps to a command-line argument: --a2009s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
aseg : a pathlike object or string representing an existing file
Input aseg file. Maps to a command-line argument: --aseg %s.
copy_inputs : a boolean
If running as a node, set this to True.This will copy the input files to the node directory.
ctxseg : a pathlike object or string representing an existing file
Maps to a command-line argument: --ctxseg %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
filled : a pathlike object or string representing an existing file
Implicit input filled file. Only required with FS v5.3.
hypo_wm : a boolean
Label hypointensities as WM. Maps to a command-line argument: --hypo-as-wm.
label_wm : a boolean
For each voxel labeled as white matter in the aseg, re-assign its label to be that of the closest cortical point if its distance is less than dmaxctx. Maps to a command-line argument: --labelwm.
rip_unknown : a boolean
Do not label WM based on ‘unknown’ corical label. Maps to a command-line argument: --rip-unknown.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
volmask : a boolean
Volume mask flag. Maps to a command-line argument: --volmask.
out_file : a pathlike object or string representing a file
Output aseg file. Maps to a command-line argument: %s.
Aparc2Aseg.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:
  • cwd (specify a folder where the interface should be run) –
  • inputs (allows the interface settings to be updated) –
Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results
Return type:

nipype.interfaces.base.support.InterfaceResult

Apas2Aseg

Link to code

Bases: FSCommand

Wrapped executable: apas2aseg.

Converts aparc+aseg.mgz into something like aseg.mgz by replacing the cortical segmentations 1000-1035 with 3 and 2000-2035 with 42. The advantage of this output is that the cortical label conforms to the actual surface (this is not the case with aseg.mgz).

Examples

>>> from nipype.interfaces.freesurfer import Apas2Aseg
>>> apas2aseg = Apas2Aseg()
>>> apas2aseg.inputs.in_file = 'aseg.mgz'
>>> apas2aseg.inputs.out_file = 'output.mgz'
>>> apas2aseg.cmdline
'apas2aseg --i aseg.mgz --o output.mgz'
in_file : a pathlike object or string representing an existing file
Input aparc+aseg.mgz. Maps to a command-line argument: --i %s.
out_file : a pathlike object or string representing a file
Output aseg file. Maps to a command-line argument: --o %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output aseg file. Maps to a command-line argument: %s.

ApplyMask

Link to code

Bases: FSCommand

Wrapped executable: mri_mask.

Use Freesurfer’s mri_mask to apply a mask to an image.

The mask file need not be binarized; it can be thresholded above a given value before application. It can also optionally be transformed into input space with an LTA matrix.

in_file : a pathlike object or string representing an existing file
Input image (will be masked). Maps to a command-line argument: %s (position: -3).
mask_file : a pathlike object or string representing an existing file
Image defining mask space. Maps to a command-line argument: %s (position: -2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
invert_xfm : a boolean
Invert transformation. Maps to a command-line argument: -invert.
keep_mask_deletion_edits : a boolean
Transfer voxel-deletion edits (voxels=1) from mask to out vol. Maps to a command-line argument: -keep_mask_deletion_edits.
mask_thresh : a float
Threshold mask before applying. Maps to a command-line argument: -T %.4f.
out_file : a pathlike object or string representing a file
Final image to write. Maps to a command-line argument: %s (position: -1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
transfer : an integer (int or long)
Transfer only voxel value # from mask to out. Maps to a command-line argument: -transfer %d.
use_abs : a boolean
Take absolute value of mask before applying. Maps to a command-line argument: -abs.
xfm_file : a pathlike object or string representing an existing file
LTA-format transformation matrix to align mask with input. Maps to a command-line argument: -xform %s.
xfm_source : a pathlike object or string representing an existing file
Image defining transform source space. Maps to a command-line argument: -lta_src %s.
xfm_target : a pathlike object or string representing an existing file
Image defining transform target space. Maps to a command-line argument: -lta_dst %s.
out_file : a pathlike object or string representing an existing file
Masked image.

CheckTalairachAlignment

Link to code

Bases: FSCommand

Wrapped executable: talairach_afd.

This program detects Talairach alignment failures

Examples

>>> from nipype.interfaces.freesurfer import CheckTalairachAlignment
>>> checker = CheckTalairachAlignment()

>>> checker.inputs.in_file = 'trans.mat'
>>> checker.inputs.threshold = 0.005
>>> checker.cmdline
'talairach_afd -T 0.005 -xfm trans.mat'

>>> checker.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Specify the talairach.xfm file to check. Maps to a command-line argument: -xfm %s (position: -1). Mutually exclusive with inputs: subject.
subject : a string
Specify subject’s name. Maps to a command-line argument: -subj %s (position: -1). Mutually exclusive with inputs: in_file.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
threshold : a float
Talairach transforms for subjects with p-values <= T are considered as very unlikely default=0.010. Maps to a command-line argument: -T %.3f. (Nipype default value: 0.01)
out_file : a pathlike object or string representing an existing file
The input file for CheckTalairachAlignment.

Contrast

Link to code

Bases: FSCommand

Wrapped executable: pctsurfcon.

Compute surface-wise gray/white contrast

Examples

>>> from nipype.interfaces.freesurfer import Contrast
>>> contrast = Contrast()
>>> contrast.inputs.subject_id = '10335'
>>> contrast.inputs.hemisphere = 'lh'
>>> contrast.inputs.white = 'lh.white' # doctest: +SKIP
>>> contrast.inputs.thickness = 'lh.thickness' # doctest: +SKIP
>>> contrast.inputs.annotation = '../label/lh.aparc.annot' # doctest: +SKIP
>>> contrast.inputs.cortex = '../label/lh.cortex.label' # doctest: +SKIP
>>> contrast.inputs.rawavg = '../mri/rawavg.mgz' # doctest: +SKIP
>>> contrast.inputs.orig = '../mri/orig.mgz' # doctest: +SKIP
>>> contrast.cmdline # doctest: +SKIP
'pctsurfcon --lh-only --s 10335'
annotation : a pathlike object or string representing an existing file
Input annotation file must be <subject_id>/label/<hemisphere>.aparc.annot.
cortex : a pathlike object or string representing an existing file
Input cortex label must be <subject_id>/label/<hemisphere>.cortex.label.
hemisphere : ‘lh’ or ‘rh’
Hemisphere being processed. Maps to a command-line argument: --%s-only.
orig : a pathlike object or string representing an existing file
Implicit input file mri/orig.mgz.
rawavg : a pathlike object or string representing an existing file
Implicit input file mri/rawavg.mgz.
subject_id : a string
Subject being processed. Maps to a command-line argument: --s %s. (Nipype default value: subject_id)
thickness : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/?h.thickness.
white : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/<hemisphere>.white.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
copy_inputs : a boolean
If running as a node, set this to True.This will copy the input files to the node directory.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_contrast : a pathlike object or string representing a file
Output contrast file from Contrast.
out_log : a pathlike object or string representing an existing file
Output log from Contrast.
out_stats : a pathlike object or string representing a file
Output stats file from Contrast.
Contrast.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:
  • cwd (specify a folder where the interface should be run) –
  • inputs (allows the interface settings to be updated) –
Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results
Return type:

nipype.interfaces.base.support.InterfaceResult

Curvature

Link to code

Bases: FSCommand

Wrapped executable: mris_curvature.

This program will compute the second fundamental form of a cortical surface. It will create two new files <hemi>.<surface>.H and <hemi>.<surface>.K with the mean and Gaussian curvature respectively.

Examples

>>> from nipype.interfaces.freesurfer import Curvature
>>> curv = Curvature()
>>> curv.inputs.in_file = 'lh.pial'
>>> curv.inputs.save = True
>>> curv.cmdline
'mris_curvature -w lh.pial'
in_file : a pathlike object or string representing an existing file
Input file for Curvature. Maps to a command-line argument: %s (position: -2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
averages : an integer (int or long)
Perform this number iterative averages of curvature measure before saving. Maps to a command-line argument: -a %d.
copy_input : a boolean
Copy input file to current directory.
distances : a tuple of the form: (an integer (int or long), an integer (int or long))
Undocumented input integer distances. Maps to a command-line argument: -distances %d %d.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
n : a boolean
Undocumented boolean flag. Maps to a command-line argument: -n.
save : a boolean
Save curvature files (will only generate screen output without this option). Maps to a command-line argument: -w.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
threshold : a float
Undocumented input threshold. Maps to a command-line argument: -thresh %.3f.
out_gauss : a pathlike object or string representing a file
Gaussian curvature output file.
out_mean : a pathlike object or string representing a file
Mean curvature output file.

CurvatureStats

Link to code

Bases: FSCommand

Wrapped executable: mris_curvature_stats.

In its simplest usage, ‘mris_curvature_stats’ will compute a set of statistics on its input <curvFile>. These statistics are the mean and standard deviation of the particular curvature on the surface, as well as the results from several surface-based integrals.

Additionally, ‘mris_curvature_stats’ can report the max/min curvature values, and compute a simple histogram based on all curvature values.

Curvatures can also be normalised and constrained to a given range before computation.

Principal curvature (K, H, k1 and k2) calculations on a surface structure can also be performed, as well as several functions derived from k1 and k2.

Finally, all output to the console, as well as any new curvatures that result from the above calculations can be saved to a series of text and binary-curvature files.

Examples

>>> from nipype.interfaces.freesurfer import CurvatureStats
>>> curvstats = CurvatureStats()
>>> curvstats.inputs.hemisphere = 'lh'
>>> curvstats.inputs.curvfile1 = 'lh.pial'
>>> curvstats.inputs.curvfile2 = 'lh.pial'
>>> curvstats.inputs.surface = 'lh.pial'
>>> curvstats.inputs.out_file = 'lh.curv.stats'
>>> curvstats.inputs.values = True
>>> curvstats.inputs.min_max = True
>>> curvstats.inputs.write = True
>>> curvstats.cmdline
'mris_curvature_stats -m -o lh.curv.stats -F pial -G --writeCurvatureFiles subject_id lh pial pial'
curvfile1 : a pathlike object or string representing an existing file
Input file for CurvatureStats. Maps to a command-line argument: %s (position: -2).
curvfile2 : a pathlike object or string representing an existing file
Input file for CurvatureStats. Maps to a command-line argument: %s (position: -1).
hemisphere : ‘lh’ or ‘rh’
Hemisphere being processed. Maps to a command-line argument: %s (position: -3).
subject_id : a string
Subject being processed. Maps to a command-line argument: %s (position: -4). (Nipype default value: subject_id)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
copy_inputs : a boolean
If running as a node, set this to True.This will copy the input files to the node directory.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
min_max : a boolean
Output min / max information for the processed curvature. Maps to a command-line argument: -m.
out_file : a pathlike object or string representing a file
Output curvature stats file. Maps to a command-line argument: -o %s.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
surface : a pathlike object or string representing an existing file
Specify surface file for CurvatureStats. Maps to a command-line argument: -F %s.
values : a boolean
Triggers a series of derived curvature values. Maps to a command-line argument: -G.
write : a boolean
Write curvature files. Maps to a command-line argument: --writeCurvatureFiles.
out_file : a pathlike object or string representing a file
Output curvature stats file.
CurvatureStats.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:
  • cwd (specify a folder where the interface should be run) –
  • inputs (allows the interface settings to be updated) –
Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results
Return type:

nipype.interfaces.base.support.InterfaceResult

EulerNumber

Link to code

Bases: FSCommand

Wrapped executable: mris_euler_number.

This program computes EulerNumber for a cortical surface

Examples

>>> from nipype.interfaces.freesurfer import EulerNumber
>>> ft = EulerNumber()
>>> ft.inputs.in_file = 'lh.pial'
>>> ft.cmdline
'mris_euler_number lh.pial'
in_file : a pathlike object or string representing an existing file
Input file for EulerNumber. Maps to a command-line argument: %s (position: -1).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
defects : an integer (int or long)
Number of defects.
euler : an integer (int or long)
Euler number of cortical surface. A value of 2 signals a topologically correct surface model with no holes.

ExtractMainComponent

Link to code

Bases: CommandLine

Wrapped executable: mris_extract_main_component.

Extract the main component of a tesselated surface

Examples

>>> from nipype.interfaces.freesurfer import ExtractMainComponent
>>> mcmp = ExtractMainComponent(in_file='lh.pial')
>>> mcmp.cmdline
'mris_extract_main_component lh.pial lh.maincmp'
in_file : a pathlike object or string representing an existing file
Input surface file. Maps to a command-line argument: %s (position: 1).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Surface containing main component. Maps to a command-line argument: %s (position: 2).
out_file : a pathlike object or string representing an existing file
Surface containing main component.

FixTopology

Link to code

Bases: FSCommand

Wrapped executable: mris_fix_topology.

This program computes a mapping from the unit sphere onto the surface of the cortex from a previously generated approximation of the cortical surface, thus guaranteeing a topologically correct surface.

Examples

>>> from nipype.interfaces.freesurfer import FixTopology
>>> ft = FixTopology()
>>> ft.inputs.in_orig = 'lh.orig' # doctest: +SKIP
>>> ft.inputs.in_inflated = 'lh.inflated' # doctest: +SKIP
>>> ft.inputs.sphere = 'lh.qsphere.nofix' # doctest: +SKIP
>>> ft.inputs.hemisphere = 'lh'
>>> ft.inputs.subject_id = '10335'
>>> ft.inputs.mgz = True
>>> ft.inputs.ga = True
>>> ft.cmdline # doctest: +SKIP
'mris_fix_topology -ga -mgz -sphere qsphere.nofix 10335 lh'
copy_inputs : a boolean
If running as a node, set this to True otherwise, the topology fixing will be done in place.
hemisphere : a string
Hemisphere being processed. Maps to a command-line argument: %s (position: -1).
in_brain : a pathlike object or string representing an existing file
Implicit input brain.mgz.
in_inflated : a pathlike object or string representing an existing file
Undocumented input file <hemisphere>.inflated.
in_orig : a pathlike object or string representing an existing file
Undocumented input file <hemisphere>.orig.
in_wm : a pathlike object or string representing an existing file
Implicit input wm.mgz.
subject_id : a string
Subject being processed. Maps to a command-line argument: %s (position: -2). (Nipype default value: subject_id)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
ga : a boolean
No documentation. Direct questions to analysis-bugs@nmr.mgh.harvard.edu. Maps to a command-line argument: -ga.
mgz : a boolean
No documentation. Direct questions to analysis-bugs@nmr.mgh.harvard.edu. Maps to a command-line argument: -mgz.
seed : an integer (int or long)
Seed for setting random number generator. Maps to a command-line argument: -seed %d.
sphere : a pathlike object or string representing a file
Sphere input file. Maps to a command-line argument: -sphere %s.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output file for FixTopology.
FixTopology.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:
  • cwd (specify a folder where the interface should be run) –
  • inputs (allows the interface settings to be updated) –
Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results
Return type:

nipype.interfaces.base.support.InterfaceResult

ImageInfo

Link to code

Bases: FSCommand

Wrapped executable: mri_info.

args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
in_file : a pathlike object or string representing an existing file
Image to query. Maps to a command-line argument: %s (position: 1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
TE : a string
Echo time (msec).
TI : a string
Inversion time (msec).
TR : a string
Repetition time(msec).
data_type : a string
Image data type.
dimensions : a tuple
Image dimensions (voxels).
file_format : a string
File format.
info : any value
Output of mri_info.
orientation : a string
Image orientation.
out_file : a pathlike object or string representing an existing file
Text file with image information.
ph_enc_dir : a string
Phase encode direction.
vox_sizes : a tuple
Voxel sizes (mm).
ImageInfo.aggregate_outputs(runtime=None, needed_outputs=None)

Collate expected outputs and apply output traits validation.

ImageInfo.info_regexp(info, field, delim='\n')

Jacobian

Link to code

Bases: FSCommand

Wrapped executable: mris_jacobian.

This program computes the Jacobian of a surface mapping.

Examples

>>> from nipype.interfaces.freesurfer import Jacobian
>>> jacobian = Jacobian()
>>> jacobian.inputs.in_origsurf = 'lh.pial'
>>> jacobian.inputs.in_mappedsurf = 'lh.pial'
>>> jacobian.cmdline
'mris_jacobian lh.pial lh.pial lh.jacobian'
in_mappedsurf : a pathlike object or string representing an existing file
Mapped surface. Maps to a command-line argument: %s (position: -2).
in_origsurf : a pathlike object or string representing an existing file
Original surface. Maps to a command-line argument: %s (position: -3).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output Jacobian of the surface mapping. Maps to a command-line argument: %s (position: -1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output Jacobian of the surface mapping.

LTAConvert

Link to code

Bases: CommandLine

Wrapped executable: lta_convert.

Convert different transformation formats. Some formats may require you to pass an image if the geometry information is missing form the transform file format.

For complete details, see the lta_convert documentation.

in_fsl : a pathlike object or string representing an existing file
Input transform of FSL type. Maps to a command-line argument: --infsl %s. Mutually exclusive with inputs: in_lta, in_fsl, in_mni, in_reg, in_niftyreg, in_itk.
in_itk : a pathlike object or string representing an existing file
Input transform of ITK type. Maps to a command-line argument: --initk %s. Mutually exclusive with inputs: in_lta, in_fsl, in_mni, in_reg, in_niftyreg, in_itk.
in_lta : a pathlike object or string representing an existing file or ‘identity.nofile’
Input transform of LTA type. Maps to a command-line argument: --inlta %s. Mutually exclusive with inputs: in_lta, in_fsl, in_mni, in_reg, in_niftyreg, in_itk.
in_mni : a pathlike object or string representing an existing file
Input transform of MNI/XFM type. Maps to a command-line argument: --inmni %s. Mutually exclusive with inputs: in_lta, in_fsl, in_mni, in_reg, in_niftyreg, in_itk.
in_niftyreg : a pathlike object or string representing an existing file
Input transform of Nifty Reg type (inverse RAS2RAS). Maps to a command-line argument: --inniftyreg %s. Mutually exclusive with inputs: in_lta, in_fsl, in_mni, in_reg, in_niftyreg, in_itk.
in_reg : a pathlike object or string representing an existing file
Input transform of TK REG type (deprecated format). Maps to a command-line argument: --inreg %s. Mutually exclusive with inputs: in_lta, in_fsl, in_mni, in_reg, in_niftyreg, in_itk.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
invert : a boolean
Maps to a command-line argument: --invert.
ltavox2vox : a boolean
Maps to a command-line argument: --ltavox2vox. Requires inputs: out_lta.
out_fsl : a boolean or a pathlike object or string representing a file
Output transform in FSL format. Maps to a command-line argument: --outfsl %s.
out_itk : a boolean or a pathlike object or string representing a file
Output transform in ITK format. Maps to a command-line argument: --outitk %s.
out_lta : a boolean or a pathlike object or string representing a file
Output linear transform (LTA Freesurfer format). Maps to a command-line argument: --outlta %s.
out_mni : a boolean or a pathlike object or string representing a file
Output transform in MNI/XFM format. Maps to a command-line argument: --outmni %s.
out_reg : a boolean or a pathlike object or string representing a file
Output transform in reg dat format. Maps to a command-line argument: --outreg %s.
source_file : a pathlike object or string representing an existing file
Maps to a command-line argument: --src %s.
target_conform : a boolean
Maps to a command-line argument: --trgconform.
target_file : a pathlike object or string representing an existing file
Maps to a command-line argument: --trg %s.
out_fsl : a pathlike object or string representing an existing file
Output transform in FSL format.
out_itk : a pathlike object or string representing an existing file
Output transform in ITK format.
out_lta : a pathlike object or string representing an existing file
Output linear transform (LTA Freesurfer format).
out_mni : a pathlike object or string representing an existing file
Output transform in MNI/XFM format.
out_reg : a pathlike object or string representing an existing file
Output transform in reg dat format.

MRIFill

Link to code

Bases: FSCommand

Wrapped executable: mri_fill.

This program creates hemispheric cutting planes and fills white matter with specific values for subsequent surface tesselation.

Examples

>>> from nipype.interfaces.freesurfer import MRIFill
>>> fill = MRIFill()
>>> fill.inputs.in_file = 'wm.mgz' # doctest: +SKIP
>>> fill.inputs.out_file = 'filled.mgz' # doctest: +SKIP
>>> fill.cmdline # doctest: +SKIP
'mri_fill wm.mgz filled.mgz'
in_file : a pathlike object or string representing an existing file
Input white matter file. Maps to a command-line argument: %s (position: -2).
out_file : a pathlike object or string representing a file
Output filled volume file name for MRIFill. Maps to a command-line argument: %s (position: -1).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
log_file : a pathlike object or string representing a file
Output log file for MRIFill. Maps to a command-line argument: -a %s.
segmentation : a pathlike object or string representing an existing file
Input segmentation file for MRIFill. Maps to a command-line argument: -segmentation %s.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
transform : a pathlike object or string representing an existing file
Input transform file for MRIFill. Maps to a command-line argument: -xform %s.
log_file : a pathlike object or string representing a file
Output log file from MRIFill.
out_file : a pathlike object or string representing a file
Output file from MRIFill.

MRIMarchingCubes

Link to code

Bases: FSCommand

Wrapped executable: mri_mc.

Uses Freesurfer’s mri_mc to create surfaces by tessellating a given input volume

Example

>>> import nipype.interfaces.freesurfer as fs
>>> mc = fs.MRIMarchingCubes()
>>> mc.inputs.in_file = 'aseg.mgz'
>>> mc.inputs.label_value = 17
>>> mc.inputs.out_file = 'lh.hippocampus'
>>> mc.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input volume to tesselate voxels from. Maps to a command-line argument: %s (position: 1).
label_value : an integer (int or long)
Label value which to tesselate from the input volume. (integer, if input is “filled.mgz” volume, 127 is rh, 255 is lh). Maps to a command-line argument: %d (position: 2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
connectivity_value : an integer (int or long)
Alter the marching cubes connectivity: 1=6+,2=18,3=6,4=26 (default=1). Maps to a command-line argument: %d (position: -1). (Nipype default value: 1)
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output filename or True to generate one. Maps to a command-line argument: ./%s (position: -2).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
surface : a pathlike object or string representing an existing file
Binary surface of the tessellation .

MRIPretess

Link to code

Bases: FSCommand

Wrapped executable: mri_pretess.

Uses Freesurfer’s mri_pretess to prepare volumes to be tessellated.

Changes white matter (WM) segmentation so that the neighbors of all voxels labeled as WM have a face in common - no edges or corners allowed.

Example

>>> import nipype.interfaces.freesurfer as fs
>>> pretess = fs.MRIPretess()
>>> pretess.inputs.in_filled = 'wm.mgz'
>>> pretess.inputs.in_norm = 'norm.mgz'
>>> pretess.inputs.nocorners = True
>>> pretess.cmdline
'mri_pretess -nocorners wm.mgz wm norm.mgz wm_pretesswm.mgz'
>>> pretess.run() # doctest: +SKIP
in_filled : a pathlike object or string representing an existing file
Filled volume, usually wm.mgz. Maps to a command-line argument: %s (position: -4).
in_norm : a pathlike object or string representing an existing file
The normalized, brain-extracted T1w image. Usually norm.mgz. Maps to a command-line argument: %s (position: -2).
label : a unicode string or an integer (int or long)
Label to be picked up, can be a Freesurfer’s string like ‘wm’ or a label value (e.g. 127 for rh or 255 for lh). Maps to a command-line argument: %s (position: -3). (Nipype default value: wm)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
keep : a boolean
Keep WM edits. Maps to a command-line argument: -keep.
nocorners : a boolean
Do not remove corner configurations in addition to edge ones. Maps to a command-line argument: -nocorners.
out_file : a pathlike object or string representing a file
The output file after mri_pretess. Maps to a command-line argument: %s (position: -1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
test : a boolean
Adds a voxel that should be removed by mri_pretess. The value of the voxel is set to that of an ON-edited WM, so it should be kept with -keep. The output will NOT be saved. Maps to a command-line argument: -test.
out_file : a pathlike object or string representing an existing file
Output file after mri_pretess.

MRITessellate

Link to code

Bases: FSCommand

Wrapped executable: mri_tessellate.

Uses Freesurfer’s mri_tessellate to create surfaces by tessellating a given input volume

Example

>>> import nipype.interfaces.freesurfer as fs
>>> tess = fs.MRITessellate()
>>> tess.inputs.in_file = 'aseg.mgz'
>>> tess.inputs.label_value = 17
>>> tess.inputs.out_file = 'lh.hippocampus'
>>> tess.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input volume to tesselate voxels from. Maps to a command-line argument: %s (position: -3).
label_value : an integer (int or long)
Label value which to tesselate from the input volume. (integer, if input is “filled.mgz” volume, 127 is rh, 255 is lh). Maps to a command-line argument: %d (position: -2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output filename or True to generate one. Maps to a command-line argument: %s (position: -1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
tesselate_all_voxels : a boolean
Tessellate the surface of all voxels with different labels. Maps to a command-line argument: -a.
use_real_RAS_coordinates : a boolean
Saves surface with real RAS coordinates where c_(r,a,s) != 0. Maps to a command-line argument: -n.
surface : a pathlike object or string representing an existing file
Binary surface of the tessellation .

MRIsCalc

Link to code

Bases: FSCommand

Wrapped executable: mris_calc.

‘mris_calc’ is a simple calculator that operates on FreeSurfer curvatures and volumes. In most cases, the calculator functions with three arguments: two inputs and an <ACTION> linking them. Some actions, however, operate with only one input <file1>. In all cases, the first input <file1> is the name of a FreeSurfer curvature overlay (e.g. rh.curv) or volume file (e.g. orig.mgz). For two inputs, the calculator first assumes that the second input is a file. If, however, this second input file doesn’t exist, the calculator assumes it refers to a float number, which is then processed according to <ACTION>.Note: <file1> and <file2> should typically be generated on the same subject.

Examples

>>> from nipype.interfaces.freesurfer import MRIsCalc
>>> example = MRIsCalc()
>>> example.inputs.in_file1 = 'lh.area' # doctest: +SKIP
>>> example.inputs.in_file2 = 'lh.area.pial' # doctest: +SKIP
>>> example.inputs.action = 'add'
>>> example.inputs.out_file = 'area.mid'
>>> example.cmdline # doctest: +SKIP
'mris_calc -o lh.area.mid lh.area add lh.area.pial'
action : a string
Action to perform on input file(s). Maps to a command-line argument: %s (position: -2).
in_file1 : a pathlike object or string representing an existing file
Input file 1. Maps to a command-line argument: %s (position: -3).
out_file : a pathlike object or string representing a file
Output file after calculation. Maps to a command-line argument: -o %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
in_file2 : a pathlike object or string representing an existing file
Input file 2. Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: in_float, in_int.
in_float : a float
Input float. Maps to a command-line argument: %f (position: -1). Mutually exclusive with inputs: in_file2, in_int.
in_int : an integer (int or long)
Input integer. Maps to a command-line argument: %d (position: -1). Mutually exclusive with inputs: in_file2, in_float.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output file after calculation.

MRIsCombine

Link to code

Bases: FSSurfaceCommand

Wrapped executable: mris_convert.

Uses Freesurfer’s mris_convert to combine two surface files into one.

For complete details, see the mris_convert Documentation.

If given an out_file that does not begin with 'lh.' or 'rh.', mris_convert will prepend 'lh.' to the file name. To avoid this behavior, consider setting out_file = './<filename>', or leaving out_file blank.

In a Node/Workflow, out_file is interpreted literally.

Example

>>> import nipype.interfaces.freesurfer as fs
>>> mris = fs.MRIsCombine()
>>> mris.inputs.in_files = ['lh.pial', 'rh.pial']
>>> mris.inputs.out_file = 'bh.pial'
>>> mris.cmdline
'mris_convert --combinesurfs lh.pial rh.pial bh.pial'
>>> mris.run()  # doctest: +SKIP
in_files : a list of from 2 to 2 items which are a pathlike object or string representing a file
Two surfaces to be combined. Maps to a command-line argument: --combinesurfs %s (position: 1).
out_file : a pathlike object or string representing a file
Output filename. Combined surfaces from in_files. Maps to a command-line argument: %s (position: -1).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing an existing file
Output filename. Combined surfaces from in_files.
MRIsCombine.normalize_filenames()

Filename normalization routine to perform only when run in Node context. Interpret out_file as a literal path to reduce surprise.

MRIsConvert

Link to code

Bases: FSCommand

Wrapped executable: mris_convert.

Uses Freesurfer’s mris_convert to convert surface files to various formats

Example

>>> import nipype.interfaces.freesurfer as fs
>>> mris = fs.MRIsConvert()
>>> mris.inputs.in_file = 'lh.pial'
>>> mris.inputs.out_datatype = 'gii'
>>> mris.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
File to read/convert. Maps to a command-line argument: %s (position: -2).
out_datatype : ‘asc’ or ‘ico’ or ‘tri’ or ‘stl’ or ‘vtk’ or ‘gii’ or ‘mgh’ or ‘mgz’
These file formats are supported: ASCII: .ascICO: .ico, .tri GEO: .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded ‘volume’: .mgh, .mgz. Mutually exclusive with inputs: out_file.
out_file : a pathlike object or string representing a file
Output filename or True to generate one. Maps to a command-line argument: %s (position: -1). Mutually exclusive with inputs: out_datatype.
annot_file : a pathlike object or string representing an existing file
Input is annotation or gifti label data. Maps to a command-line argument: --annot %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
dataarray_num : an integer (int or long)
If input is gifti, ‘num’ specifies which data array to use. Maps to a command-line argument: --da_num %d.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
functional_file : a pathlike object or string representing an existing file
Input is functional time-series or other multi-frame data (must specify surface). Maps to a command-line argument: -f %s.
label_file : a pathlike object or string representing an existing file
Infile is .label file, label is name of this label. Maps to a command-line argument: --label %s.
labelstats_outfile : a pathlike object or string representing a file
Outfile is name of gifti file to which label stats will be written. Maps to a command-line argument: --labelstats %s.
normal : a boolean
Output is an ascii file where vertex data. Maps to a command-line argument: -n.
origname : a string
Read orig positions. Maps to a command-line argument: -o %s.
parcstats_file : a pathlike object or string representing an existing file
Infile is name of text file containing label/val pairs. Maps to a command-line argument: --parcstats %s.
patch : a boolean
Input is a patch, not a full surface. Maps to a command-line argument: -p.
rescale : a boolean
Rescale vertex xyz so total area is same as group average. Maps to a command-line argument: -r.
scalarcurv_file : a pathlike object or string representing an existing file
Input is scalar curv overlay file (must still specify surface). Maps to a command-line argument: -c %s.
scale : a float
Scale vertex xyz by scale. Maps to a command-line argument: -s %.3f.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
talairachxfm_subjid : a string
Apply talairach xfm of subject to vertex xyz. Maps to a command-line argument: -t %s.
to_scanner : a boolean
Convert coordinates from native FS (tkr) coords to scanner coords. Maps to a command-line argument: --to-scanner.
to_tkr : a boolean
Convert coordinates from scanner coords to native FS (tkr) coords. Maps to a command-line argument: --to-tkr.
vertex : a boolean
Writes out neighbors of a vertex in each row. Maps to a command-line argument: -v.
xyz_ascii : a boolean
Print only surface xyz to ascii file. Maps to a command-line argument: -a.
converted : a pathlike object or string representing an existing file
Converted output surface.

MRIsExpand

Link to code

Bases: FSSurfaceCommand

Wrapped executable: mris_expand.

Expands a surface (typically ?h.white) outwards while maintaining smoothness and self-intersection constraints.

Examples

>>> from nipype.interfaces.freesurfer import MRIsExpand
>>> mris_expand = MRIsExpand(thickness=True, distance=0.5)
>>> mris_expand.inputs.in_file = 'lh.white'
>>> mris_expand.cmdline
'mris_expand -thickness lh.white 0.5 expanded'
>>> mris_expand.inputs.out_name = 'graymid'
>>> mris_expand.cmdline
'mris_expand -thickness lh.white 0.5 graymid'
distance : a float
Distance in mm or fraction of cortical thickness. Maps to a command-line argument: %g (position: -2).
in_file : a pathlike object or string representing an existing file
Surface to expand. Maps to a command-line argument: %s (position: -3).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
dt : a float
Dt (implicit: 0.25). Maps to a command-line argument: -T %g.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
nsurfaces : an integer (int or long)
Number of surfacces to write during expansion. Maps to a command-line argument: -N %d.
out_name : a unicode string
Output surface file. If no path, uses directory of in_file. If no path AND missing “lh.” or “rh.”, derive from in_file. Maps to a command-line argument: %s (position: -1). (Nipype default value: expanded)
pial : a unicode string
Name of pial file (implicit: “pial”) If no path, uses directory of in_file If no path AND missing “lh.” or “rh.”, derive from in_file. Maps to a command-line argument: -pial %s.
smooth_averages : an integer (int or long)
Smooth surface with N iterations after expansion. Maps to a command-line argument: -A %d.
sphere : a unicode string
WARNING: Do not change this trait. (Nipype default value: sphere)
spring : a float
Spring term (implicit: 0.05). Maps to a command-line argument: -S %g.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
thickness : a boolean
Expand by fraction of cortical thickness, not mm. Maps to a command-line argument: -thickness.
thickness_name : a unicode string
Name of thickness file (implicit: “thickness”) If no path, uses directory of in_file If no path AND missing “lh.” or “rh.”, derive from in_file. Maps to a command-line argument: -thickness_name %s.
write_iterations : an integer (int or long)
Write snapshots of expansion every N iterations. Maps to a command-line argument: -W %d.
out_file : a pathlike object or string representing a file
Output surface file.
MRIsExpand.normalize_filenames()

Filename normalization routine to perform only when run in Node context. Find full paths for pial, thickness and sphere files for copying.

MRIsInflate

Link to code

Bases: FSCommand

Wrapped executable: mris_inflate.

This program will inflate a cortical surface.

Examples

>>> from nipype.interfaces.freesurfer import MRIsInflate
>>> inflate = MRIsInflate()
>>> inflate.inputs.in_file = 'lh.pial'
>>> inflate.inputs.no_save_sulc = True
>>> inflate.cmdline # doctest: +SKIP
'mris_inflate -no-save-sulc lh.pial lh.inflated'
in_file : a pathlike object or string representing an existing file
Input file for MRIsInflate. Maps to a command-line argument: %s (position: -2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
no_save_sulc : a boolean
Do not save sulc file as output. Maps to a command-line argument: -no-save-sulc. Mutually exclusive with inputs: out_sulc.
out_file : a pathlike object or string representing a file
Output file for MRIsInflate. Maps to a command-line argument: %s (position: -1).
out_sulc : a pathlike object or string representing a file
Output sulc file. Mutually exclusive with inputs: no_save_sulc.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output file for MRIsInflate.
out_sulc : a pathlike object or string representing a file
Output sulc file.

MakeAverageSubject

Link to code

Bases: FSCommand

Wrapped executable: make_average_subject.

Make an average freesurfer subject

Examples

>>> from nipype.interfaces.freesurfer import MakeAverageSubject
>>> avg = MakeAverageSubject(subjects_ids=['s1', 's2'])
>>> avg.cmdline
'make_average_subject --out average --subjects s1 s2'
subjects_ids : a list of items which are a unicode string
Freesurfer subjects ids to average. Maps to a command-line argument: --subjects %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_name : a pathlike object or string representing a file
Name for the average subject. Maps to a command-line argument: --out %s. (Nipype default value: average)
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
average_subject_name : a unicode string
Output registration file.

MakeSurfaces

Link to code

Bases: FSCommand

Wrapped executable: mris_make_surfaces.

This program positions the tessellation of the cortical surface at the white matter surface, then the gray matter surface and generate surface files for these surfaces as well as a ‘curvature’ file for the cortical thickness, and a surface file which approximates layer IV of the cortical sheet.

Examples

>>> from nipype.interfaces.freesurfer import MakeSurfaces
>>> makesurfaces = MakeSurfaces()
>>> makesurfaces.inputs.hemisphere = 'lh'
>>> makesurfaces.inputs.subject_id = '10335'
>>> makesurfaces.inputs.in_orig = 'lh.pial'
>>> makesurfaces.inputs.in_wm = 'wm.mgz'
>>> makesurfaces.inputs.in_filled = 'norm.mgz'
>>> makesurfaces.inputs.in_label = 'aparc+aseg.nii'
>>> makesurfaces.inputs.in_T1 = 'T1.mgz'
>>> makesurfaces.inputs.orig_pial = 'lh.pial'
>>> makesurfaces.cmdline
'mris_make_surfaces -T1 T1.mgz -orig pial -orig_pial pial 10335 lh'
hemisphere : ‘lh’ or ‘rh’
Hemisphere being processed. Maps to a command-line argument: %s (position: -1).
in_filled : a pathlike object or string representing an existing file
Implicit input file filled.mgz.
in_orig : a pathlike object or string representing an existing file
Implicit input file <hemisphere>.orig. Maps to a command-line argument: -orig %s.
in_wm : a pathlike object or string representing an existing file
Implicit input file wm.mgz.
subject_id : a string
Subject being processed. Maps to a command-line argument: %s (position: -2). (Nipype default value: subject_id)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
copy_inputs : a boolean
If running as a node, set this to True.This will copy the input files to the node directory.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
fix_mtl : a boolean
Undocumented flag. Maps to a command-line argument: -fix_mtl.
in_T1 : a pathlike object or string representing an existing file
Input brain or T1 file. Maps to a command-line argument: -T1 %s.
in_aseg : a pathlike object or string representing an existing file
Input segmentation file. Maps to a command-line argument: -aseg %s.
in_label : a pathlike object or string representing an existing file
Implicit input label/<hemisphere>.aparc.annot. Mutually exclusive with inputs: noaparc.
in_white : a pathlike object or string representing an existing file
Implicit input that is sometimes used.
longitudinal : a boolean
No documentation (used for longitudinal processing). Maps to a command-line argument: -long.
maximum : a float
No documentation (used for longitudinal processing). Maps to a command-line argument: -max %.1f.
mgz : a boolean
No documentation. Direct questions to analysis-bugs@nmr.mgh.harvard.edu. Maps to a command-line argument: -mgz.
no_white : a boolean
Undocumented flag. Maps to a command-line argument: -nowhite.
noaparc : a boolean
No documentation. Direct questions to analysis-bugs@nmr.mgh.harvard.edu. Maps to a command-line argument: -noaparc. Mutually exclusive with inputs: in_label.
orig_pial : a pathlike object or string representing an existing file
Specify a pial surface to start with. Maps to a command-line argument: -orig_pial %s. Requires inputs: in_label.
orig_white : a pathlike object or string representing an existing file
Specify a white surface to start with. Maps to a command-line argument: -orig_white %s.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
white : a string
White surface name. Maps to a command-line argument: -white %s.
white_only : a boolean
Undocumented flage. Maps to a command-line argument: -whiteonly.
out_area : a pathlike object or string representing a file
Output area file for MakeSurfaces.
out_cortex : a pathlike object or string representing a file
Output cortex file for MakeSurfaces.
out_curv : a pathlike object or string representing a file
Output curv file for MakeSurfaces.
out_pial : a pathlike object or string representing a file
Output pial surface for MakeSurfaces.
out_thickness : a pathlike object or string representing a file
Output thickness file for MakeSurfaces.
out_white : a pathlike object or string representing a file
Output white matter hemisphere surface.
MakeSurfaces.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:
  • cwd (specify a folder where the interface should be run) –
  • inputs (allows the interface settings to be updated) –
Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results
Return type:

nipype.interfaces.base.support.InterfaceResult

ParcellationStats

Link to code

Bases: FSCommand

Wrapped executable: mris_anatomical_stats.

This program computes a number of anatomical properties.

Examples

>>> from nipype.interfaces.freesurfer import ParcellationStats
>>> import os
>>> parcstats = ParcellationStats()
>>> parcstats.inputs.subject_id = '10335'
>>> parcstats.inputs.hemisphere = 'lh'
>>> parcstats.inputs.wm = './../mri/wm.mgz' # doctest: +SKIP
>>> parcstats.inputs.transform = './../mri/transforms/talairach.xfm' # doctest: +SKIP
>>> parcstats.inputs.brainmask = './../mri/brainmask.mgz' # doctest: +SKIP
>>> parcstats.inputs.aseg = './../mri/aseg.presurf.mgz' # doctest: +SKIP
>>> parcstats.inputs.ribbon = './../mri/ribbon.mgz' # doctest: +SKIP
>>> parcstats.inputs.lh_pial = 'lh.pial' # doctest: +SKIP
>>> parcstats.inputs.rh_pial = 'lh.pial' # doctest: +SKIP
>>> parcstats.inputs.lh_white = 'lh.white' # doctest: +SKIP
>>> parcstats.inputs.rh_white = 'rh.white' # doctest: +SKIP
>>> parcstats.inputs.thickness = 'lh.thickness' # doctest: +SKIP
>>> parcstats.inputs.surface = 'white'
>>> parcstats.inputs.out_table = 'lh.test.stats'
>>> parcstats.inputs.out_color = 'test.ctab'
>>> parcstats.cmdline # doctest: +SKIP
'mris_anatomical_stats -c test.ctab -f lh.test.stats 10335 lh white'
aseg : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/aseg.presurf.mgz.
brainmask : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/brainmask.mgz.
hemisphere : ‘lh’ or ‘rh’
Hemisphere being processed. Maps to a command-line argument: %s (position: -2).
lh_pial : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/lh.pial.
lh_white : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/lh.white.
rh_pial : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/rh.pial.
rh_white : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/rh.white.
ribbon : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/ribbon.mgz.
subject_id : a string
Subject being processed. Maps to a command-line argument: %s (position: -3). (Nipype default value: subject_id)
thickness : a pathlike object or string representing an existing file
Input file must be <subject_id>/surf/?h.thickness.
transform : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/transforms/talairach.xfm.
wm : a pathlike object or string representing an existing file
Input file must be <subject_id>/mri/wm.mgz.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
copy_inputs : a boolean
If running as a node, set this to True.This will copy the input files to the node directory.
cortex_label : a pathlike object or string representing an existing file
Implicit input file {hemi}.cortex.label.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
in_annotation : a pathlike object or string representing an existing file
Compute properties for each label in the annotation file separately. Maps to a command-line argument: -a %s. Mutually exclusive with inputs: in_label.
in_cortex : a pathlike object or string representing an existing file
Input cortex label. Maps to a command-line argument: -cortex %s.
in_label : a pathlike object or string representing an existing file
Limit calculations to specified label. Maps to a command-line argument: -l %s. Mutually exclusive with inputs: in_annotatoin, out_color.
mgz : a boolean
Look for mgz files. Maps to a command-line argument: -mgz.
out_color : a pathlike object or string representing a file
Output annotation files’s colortable to text file. Maps to a command-line argument: -c %s. Mutually exclusive with inputs: in_label.
out_table : a pathlike object or string representing a file
Table output to tablefile. Maps to a command-line argument: -f %s. Requires inputs: tabular_output.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
surface : a string
Input surface (e.g. ‘white’). Maps to a command-line argument: %s (position: -1).
tabular_output : a boolean
Tabular output. Maps to a command-line argument: -b.
th3 : a boolean
Turns on new vertex-wise volume calc for mris_anat_stats. Maps to a command-line argument: -th3. Requires inputs: cortex_label.
out_color : a pathlike object or string representing a file
Output annotation files’s colortable to text file.
out_table : a pathlike object or string representing a file
Table output to tablefile.
ParcellationStats.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:
  • cwd (specify a folder where the interface should be run) –
  • inputs (allows the interface settings to be updated) –
Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results
Return type:

nipype.interfaces.base.support.InterfaceResult

RelabelHypointensities

Link to code

Bases: FSCommand

Wrapped executable: mri_relabel_hypointensities.

Relabel Hypointensities

Examples

>>> from nipype.interfaces.freesurfer import RelabelHypointensities
>>> relabelhypos = RelabelHypointensities()
>>> relabelhypos.inputs.lh_white = 'lh.pial'
>>> relabelhypos.inputs.rh_white = 'lh.pial'
>>> relabelhypos.inputs.surf_directory = '.'
>>> relabelhypos.inputs.aseg = 'aseg.mgz'
>>> relabelhypos.cmdline
'mri_relabel_hypointensities aseg.mgz . aseg.hypos.mgz'
aseg : a pathlike object or string representing an existing file
Input aseg file. Maps to a command-line argument: %s (position: -3).
lh_white : a pathlike object or string representing an existing file
Implicit input file must be lh.white.
rh_white : a pathlike object or string representing an existing file
Implicit input file must be rh.white.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output aseg file. Maps to a command-line argument: %s (position: -1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
surf_directory : a pathlike object or string representing an existing directory
Directory containing lh.white and rh.white. Maps to a command-line argument: %s (position: -2). (Nipype default value: .)
out_file : a pathlike object or string representing a file
Output aseg file. Maps to a command-line argument: %s.

RemoveIntersection

Link to code

Bases: FSCommand

Wrapped executable: mris_remove_intersection.

This program removes the intersection of the given MRI

Examples

>>> from nipype.interfaces.freesurfer import RemoveIntersection
>>> ri = RemoveIntersection()
>>> ri.inputs.in_file = 'lh.pial'
>>> ri.cmdline
'mris_remove_intersection lh.pial lh.pial'
in_file : a pathlike object or string representing an existing file
Input file for RemoveIntersection. Maps to a command-line argument: %s (position: -2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output file for RemoveIntersection. Maps to a command-line argument: %s (position: -1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output file for RemoveIntersection.

RemoveNeck

Link to code

Bases: FSCommand

Wrapped executable: mri_remove_neck.

Crops the neck out of the mri image

Examples

>>> from nipype.interfaces.freesurfer import TalairachQC
>>> remove_neck = RemoveNeck()
>>> remove_neck.inputs.in_file = 'norm.mgz'
>>> remove_neck.inputs.transform = 'trans.mat'
>>> remove_neck.inputs.template = 'trans.mat'
>>> remove_neck.cmdline
'mri_remove_neck norm.mgz trans.mat trans.mat norm_noneck.mgz'
in_file : a pathlike object or string representing an existing file
Input file for RemoveNeck. Maps to a command-line argument: %s (position: -4).
template : a pathlike object or string representing an existing file
Input template file for RemoveNeck. Maps to a command-line argument: %s (position: -2).
transform : a pathlike object or string representing an existing file
Input transform file for RemoveNeck. Maps to a command-line argument: %s (position: -3).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Output file for RemoveNeck. Maps to a command-line argument: %s (position: -1).
radius : an integer (int or long)
Radius. Maps to a command-line argument: -radius %d.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output file with neck removed.

SampleToSurface

Link to code

Bases: FSCommand

Wrapped executable: mri_vol2surf.

Sample a volume to the cortical surface using Freesurfer’s mri_vol2surf.

You must supply a sampling method, range, and units. You can project either a given distance (in mm) or a given fraction of the cortical thickness at that vertex along the surface normal from the target surface, and then set the value of that vertex to be either the value at that point or the average or maximum value found along the projection vector.

By default, the surface will be saved as a vector with a length equal to the number of vertices on the target surface. This is not a problem for Freesurfer programs, but if you intend to use the file with interfaces to another package, you must set the reshape input to True, which will factor the surface vector into a matrix with dimensions compatible with proper Nifti files.

Examples

>>> import nipype.interfaces.freesurfer as fs
>>> sampler = fs.SampleToSurface(hemi="lh")
>>> sampler.inputs.source_file = "cope1.nii.gz"
>>> sampler.inputs.reg_file = "register.dat"
>>> sampler.inputs.sampling_method = "average"
>>> sampler.inputs.sampling_range = 1
>>> sampler.inputs.sampling_units = "frac"
>>> sampler.cmdline  # doctest: +ELLIPSIS
'mri_vol2surf --hemi lh --o ...lh.cope1.mgz --reg register.dat --projfrac-avg 1.000 --mov cope1.nii.gz'
>>> res = sampler.run() # doctest: +SKIP
hemi : ‘lh’ or ‘rh’
Target hemisphere. Maps to a command-line argument: --hemi %s.
mni152reg : a boolean
Source volume is in MNI152 space. Maps to a command-line argument: --mni152reg. Mutually exclusive with inputs: reg_file, reg_header, mni152reg.
projection_stem : a string
Stem for precomputed linear estimates and volume fractions. Mutually exclusive with inputs: sampling_method.
reg_file : a pathlike object or string representing an existing file
Source-to-reference registration file. Maps to a command-line argument: --reg %s. Mutually exclusive with inputs: reg_file, reg_header, mni152reg.
reg_header : a boolean
Register based on header geometry. Maps to a command-line argument: --regheader %s. Mutually exclusive with inputs: reg_file, reg_header, mni152reg. Requires inputs: subject_id.
sampling_method : ‘point’ or ‘max’ or ‘average’
How to sample – at a point or at the max or average over a range. Maps to a command-line argument: %s. Mutually exclusive with inputs: projection_stem. Requires inputs: sampling_range, sampling_units.
source_file : a pathlike object or string representing an existing file
Volume to sample values from. Maps to a command-line argument: --mov %s.
apply_rot : a tuple of the form: (a float, a float, a float)
Rotation angles (in degrees) to apply to reg matrix. Maps to a command-line argument: --rot %.3f %.3f %.3f.
apply_trans : a tuple of the form: (a float, a float, a float)
Translation (in mm) to apply to reg matrix. Maps to a command-line argument: --trans %.3f %.3f %.3f.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
cortex_mask : a boolean
Mask the target surface with hemi.cortex.label. Maps to a command-line argument: --cortex. Mutually exclusive with inputs: mask_label.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
fix_tk_reg : a boolean
Make reg matrix round-compatible. Maps to a command-line argument: --fixtkreg.
float2int_method : ‘round’ or ‘tkregister’
Method to convert reg matrix values (default is round). Maps to a command-line argument: --float2int %s.
frame : an integer (int or long)
Save only one frame (0-based). Maps to a command-line argument: --frame %d.
hits_file : a boolean or a pathlike object or string representing an existing file
Save image with number of hits at each voxel. Maps to a command-line argument: --srchit %s.
hits_type : ‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’
Hits file type. Maps to a command-line argument: --srchit_type.
ico_order : an integer (int or long)
Icosahedron order when target_subject is ‘ico’. Maps to a command-line argument: --icoorder %d. Requires inputs: target_subject.
interp_method : ‘nearest’ or ‘trilinear’
Interpolation method. Maps to a command-line argument: --interp %s.
mask_label : a pathlike object or string representing an existing file
Label file to mask output with. Maps to a command-line argument: --mask %s. Mutually exclusive with inputs: cortex_mask.
no_reshape : a boolean
Do not reshape surface vector (default). Maps to a command-line argument: --noreshape. Mutually exclusive with inputs: reshape.
out_file : a pathlike object or string representing a file
Surface file to write. Maps to a command-line argument: --o %s.
out_type : ‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’ or ‘gii’
Output file type. Maps to a command-line argument: --out_type %s.
override_reg_subj : a boolean
Override the subject in the reg file header. Maps to a command-line argument: --srcsubject %s. Requires inputs: subject_id.
reference_file : a pathlike object or string representing an existing file
Reference volume (default is orig.mgz). Maps to a command-line argument: --ref %s.
reshape : a boolean
Reshape surface vector to fit in non-mgh format. Maps to a command-line argument: --reshape. Mutually exclusive with inputs: no_reshape.
reshape_slices : an integer (int or long)
Number of ‘slices’ for reshaping. Maps to a command-line argument: --rf %d.
sampling_range : a float or a tuple of the form: (a float, a float, a float)
Sampling range - a point or a tuple of (min, max, step).
sampling_units : ‘mm’ or ‘frac’
Sampling range type – either ‘mm’ or ‘frac’.
scale_input : a float
Multiple all intensities by scale factor. Maps to a command-line argument: --scale %.3f.
smooth_surf : a float
Smooth output surface (mm fwhm). Maps to a command-line argument: --surf-fwhm %.3f.
smooth_vol : a float
Smooth input volume (mm fwhm). Maps to a command-line argument: --fwhm %.3f.
subject_id : a string
Subject id.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
surf_reg : a boolean or a unicode string
Use surface registration to target subject. Maps to a command-line argument: --surfreg %s. Requires inputs: target_subject.
surface : a string
Target surface (default is white). Maps to a command-line argument: --surf %s.
target_subject : a string
Sample to surface of different subject than source. Maps to a command-line argument: --trgsubject %s.
vox_file : a boolean or a pathlike object or string representing a file
Text file with the number of voxels intersecting the surface. Maps to a command-line argument: --nvox %s.
hits_file : a pathlike object or string representing an existing file
Image with number of hits at each voxel.
out_file : a pathlike object or string representing an existing file
Surface file.
vox_file : a pathlike object or string representing an existing file
Text file with the number of voxels intersecting the surface.

SmoothTessellation

Link to code

Bases: FSCommand

Wrapped executable: mris_smooth.

Smooth a tessellated surface.

See also

nipype.interfaces.freesurfer.utils.SurfaceSmooth interface for smoothing a scalar field along a surface manifold

Example

>>> import nipype.interfaces.freesurfer as fs
>>> smooth = fs.SmoothTessellation()
>>> smooth.inputs.in_file = 'lh.hippocampus.stl'
>>> smooth.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input volume to tesselate voxels from. Maps to a command-line argument: %s (position: -2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
curvature_averaging_iterations : an integer (int or long)
Number of curvature averaging iterations (default=10). Maps to a command-line argument: -a %d.
disable_estimates : a boolean
Disables the writing of curvature and area estimates. Maps to a command-line argument: -nw.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
gaussian_curvature_norm_steps : an integer (int or long)
Use Gaussian curvature smoothing. Maps to a command-line argument: %d.
gaussian_curvature_smoothing_steps : an integer (int or long)
Use Gaussian curvature smoothing. Maps to a command-line argument: %d.
normalize_area : a boolean
Normalizes the area after smoothing. Maps to a command-line argument: -area.
out_area_file : a pathlike object or string representing a file
Write area to ?h.areaname (default “area”). Maps to a command-line argument: -b %s.
out_curvature_file : a pathlike object or string representing a file
Write curvature to ?h.curvname (default “curv”). Maps to a command-line argument: -c %s.
out_file : a pathlike object or string representing a file
Output filename or True to generate one. Maps to a command-line argument: %s (position: -1).
seed : an integer (int or long)
Seed for setting random number generator. Maps to a command-line argument: -seed %d.
smoothing_iterations : an integer (int or long)
Number of smoothing iterations (default=10). Maps to a command-line argument: -n %d.
snapshot_writing_iterations : an integer (int or long)
Write snapshot every n iterations. Maps to a command-line argument: -w %d.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
use_gaussian_curvature_smoothing : a boolean
Use Gaussian curvature smoothing. Maps to a command-line argument: -g.
use_momentum : a boolean
Uses momentum. Maps to a command-line argument: -m.
surface : a pathlike object or string representing an existing file
Smoothed surface file.

Sphere

Link to code

Bases: FSCommandOpenMP

Wrapped executable: mris_sphere.

This program will add a template into an average surface

Examples

>>> from nipype.interfaces.freesurfer import Sphere
>>> sphere = Sphere()
>>> sphere.inputs.in_file = 'lh.pial'
>>> sphere.cmdline
'mris_sphere lh.pial lh.sphere'
in_file : a pathlike object or string representing an existing file
Input file for Sphere. Maps to a command-line argument: %s (position: -2).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
in_smoothwm : a pathlike object or string representing an existing file
Input surface required when -q flag is not selected.
magic : a boolean
No documentation. Direct questions to analysis-bugs@nmr.mgh.harvard.edu. Maps to a command-line argument: -q.
num_threads : an integer (int or long)
Allows for specifying more threads.
out_file : a pathlike object or string representing a file
Output file for Sphere. Maps to a command-line argument: %s (position: -1).
seed : an integer (int or long)
Seed for setting random number generator. Maps to a command-line argument: -seed %d.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
Output file for Sphere.

Surface2VolTransform

Link to code

Bases: FSCommand

Wrapped executable: mri_surf2vol.

Use FreeSurfer mri_surf2vol to apply a transform.

Examples

>>> from nipype.interfaces.freesurfer import Surface2VolTransform
>>> xfm2vol = Surface2VolTransform()
>>> xfm2vol.inputs.source_file = 'lh.cope1.mgz'
>>> xfm2vol.inputs.reg_file = 'register.mat'
>>> xfm2vol.inputs.hemi = 'lh'
>>> xfm2vol.inputs.template_file = 'cope1.nii.gz'
>>> xfm2vol.inputs.subjects_dir = '.'
>>> xfm2vol.cmdline
'mri_surf2vol --hemi lh --volreg register.mat --surfval lh.cope1.mgz --sd . --template cope1.nii.gz --outvol lh.cope1_asVol.nii --vtxvol lh.cope1_asVol_vertex.nii'
>>> res = xfm2vol.run()# doctest: +SKIP
hemi : a unicode string
Hemisphere of data. Maps to a command-line argument: --hemi %s.
reg_file : a pathlike object or string representing an existing file
TkRAS-to-tkRAS matrix (tkregister2 format). Maps to a command-line argument: --volreg %s. Mutually exclusive with inputs: subject_id.
source_file : a pathlike object or string representing an existing file
This is the source of the surface values. Maps to a command-line argument: --surfval %s. Mutually exclusive with inputs: mkmask.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
mkmask : a boolean
Make a mask instead of loading surface values. Maps to a command-line argument: --mkmask. Mutually exclusive with inputs: source_file.
projfrac : a float
Thickness fraction. Maps to a command-line argument: --projfrac %s.
subject_id : a unicode string
Subject id. Maps to a command-line argument: --identity %s. Mutually exclusive with inputs: reg_file.
subjects_dir : a unicode string
Freesurfer subjects directory defaults to $SUBJECTS_DIR. Maps to a command-line argument: --sd %s.
surf_name : a unicode string
Surfname (default is white). Maps to a command-line argument: --surf %s.
template_file : a pathlike object or string representing an existing file
Output template volume. Maps to a command-line argument: --template %s.
transformed_file : a pathlike object or string representing a file
Output volume. Maps to a command-line argument: --outvol %s.
vertexvol_file : a pathlike object or string representing a file
Path name of the vertex output volume, which is the same as output volume except that the value of each voxel is the vertex-id that is mapped to that voxel. Maps to a command-line argument: --vtxvol %s.
transformed_file : a pathlike object or string representing an existing file
Path to output file if used normally.
vertexvol_file : a pathlike object or string representing a file
Vertex map volume path id. Optional.

SurfaceSmooth

Link to code

Bases: FSCommand

Wrapped executable: mri_surf2surf.

Smooth a surface image with mri_surf2surf.

The surface is smoothed by an interative process of averaging the value at each vertex with those of its adjacent neighbors. You may supply either the number of iterations to run or a desired effective FWHM of the smoothing process. If the latter, the underlying program will calculate the correct number of iterations internally.

See also

nipype.interfaces.freesurfer.utils.SmoothTessellation interface for smoothing a tessellated surface (e.g. in gifti or .stl)

Examples

>>> import nipype.interfaces.freesurfer as fs
>>> smoother = fs.SurfaceSmooth()
>>> smoother.inputs.in_file = "lh.cope1.mgz"
>>> smoother.inputs.subject_id = "subj_1"
>>> smoother.inputs.hemi = "lh"
>>> smoother.inputs.fwhm = 5
>>> smoother.cmdline # doctest: +ELLIPSIS
'mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval lh.cope1.mgz --tval ...lh.cope1_smooth5.mgz --s subj_1'
>>> smoother.run() # doctest: +SKIP
hemi : ‘lh’ or ‘rh’
Hemisphere to operate on. Maps to a command-line argument: --hemi %s.
in_file : a pathlike object or string representing a file
Source surface file. Maps to a command-line argument: --sval %s.
subject_id : a string
Subject id of surface file. Maps to a command-line argument: --s %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
cortex : a boolean
Only smooth within $hemi.cortex.label. Maps to a command-line argument: --cortex. (Nipype default value: True)
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
fwhm : a float
Effective FWHM of the smoothing process. Maps to a command-line argument: --fwhm %.4f. Mutually exclusive with inputs: smooth_iters.
out_file : a pathlike object or string representing a file
Surface file to write. Maps to a command-line argument: --tval %s.
reshape : a boolean
Reshape surface vector to fit in non-mgh format. Maps to a command-line argument: --reshape.
smooth_iters : an integer (int or long)
Iterations of the smoothing process. Maps to a command-line argument: --smooth %d. Mutually exclusive with inputs: fwhm.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing an existing file
Smoothed surface file.

SurfaceSnapshots

Link to code

Bases: FSCommand

Wrapped executable: tksurfer.

Use Tksurfer to save pictures of the cortical surface.

By default, this takes snapshots of the lateral, medial, ventral, and dorsal surfaces. See the six_images option to add the anterior and posterior surfaces.

You may also supply your own tcl script (see the Freesurfer wiki for information on scripting tksurfer). The screenshot stem is set as the environment variable “_SNAPSHOT_STEM”, which you can use in your own scripts.

Node that this interface will not run if you do not have graphics enabled on your system.

Examples

>>> import nipype.interfaces.freesurfer as fs
>>> shots = fs.SurfaceSnapshots(subject_id="fsaverage", hemi="lh", surface="pial")
>>> shots.inputs.overlay = "zstat1.nii.gz"
>>> shots.inputs.overlay_range = (2.3, 6)
>>> shots.inputs.overlay_reg = "register.dat"
>>> res = shots.run() # doctest: +SKIP
hemi : ‘lh’ or ‘rh’
Hemisphere to visualize. Maps to a command-line argument: %s (position: 2).
subject_id : a string
Subject to visualize. Maps to a command-line argument: %s (position: 1).
surface : a string
Surface to visualize. Maps to a command-line argument: %s (position: 3).
annot_file : a pathlike object or string representing an existing file
Path to annotation file to display. Maps to a command-line argument: -annotation %s. Mutually exclusive with inputs: annot_name.
annot_name : a string
Name of annotation to display (must be in $subject/label directory. Maps to a command-line argument: -annotation %s. Mutually exclusive with inputs: annot_file.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
colortable : a pathlike object or string representing an existing file
Load colortable file. Maps to a command-line argument: -colortable %s.
demean_overlay : a boolean
Remove mean from overlay. Maps to a command-line argument: -zm.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
identity_reg : a boolean
Use the identity matrix to register the overlay to the surface. Maps to a command-line argument: -overlay-reg-identity. Mutually exclusive with inputs: overlay_reg, identity_reg, mni152_reg.
invert_overlay : a boolean
Invert the overlay display. Maps to a command-line argument: -invphaseflag 1.
label_file : a pathlike object or string representing an existing file
Path to label file to display. Maps to a command-line argument: -label %s. Mutually exclusive with inputs: label_name.
label_name : a string
Name of label to display (must be in $subject/label directory. Maps to a command-line argument: -label %s. Mutually exclusive with inputs: label_file.
label_outline : a boolean
Draw label/annotation as outline. Maps to a command-line argument: -label-outline.
label_under : a boolean
Draw label/annotation under overlay. Maps to a command-line argument: -labels-under.
mni152_reg : a boolean
Use to display a volume in MNI152 space on the average subject. Maps to a command-line argument: -mni152reg. Mutually exclusive with inputs: overlay_reg, identity_reg, mni152_reg.
orig_suffix : a string
Set the orig surface suffix string. Maps to a command-line argument: -orig %s.
overlay : a pathlike object or string representing an existing file
Load an overlay volume/surface. Maps to a command-line argument: -overlay %s. Requires inputs: overlay_range.
overlay_range : a float or a tuple of the form: (a float, a float) or a tuple of the form: (a float, a float, a float)
Overlay range–either min, (min, max) or (min, mid, max). Maps to a command-line argument: %s.
overlay_range_offset : a float
Overlay range will be symettric around offset value. Maps to a command-line argument: -foffset %.3f.
overlay_reg : a pathlike object or string representing an existing file
Registration matrix file to register overlay to surface. Maps to a command-line argument: -overlay-reg %s. Mutually exclusive with inputs: overlay_reg, identity_reg, mni152_reg.
patch_file : a pathlike object or string representing an existing file
Load a patch. Maps to a command-line argument: -patch %s.
reverse_overlay : a boolean
Reverse the overlay display. Maps to a command-line argument: -revphaseflag 1.
screenshot_stem : a string
Stem to use for screenshot file names.
show_color_scale : a boolean
Display the color scale bar. Maps to a command-line argument: -colscalebarflag 1.
show_color_text : a boolean
Display text in the color scale bar. Maps to a command-line argument: -colscaletext 1.
show_curv : a boolean
Show curvature. Maps to a command-line argument: -curv. Mutually exclusive with inputs: show_gray_curv.
show_gray_curv : a boolean
Show curvature in gray. Maps to a command-line argument: -gray. Mutually exclusive with inputs: show_curv.
six_images : a boolean
Also take anterior and posterior snapshots.
sphere_suffix : a string
Set the sphere.reg suffix string. Maps to a command-line argument: -sphere %s.
stem_template_args : a list of items which are a string
Input names to use as arguments for a string-formated stem template. Requires inputs: screenshot_stem.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
tcl_script : a pathlike object or string representing an existing file
Override default screenshot script. Maps to a command-line argument: %s.
truncate_overlay : a boolean
Truncate the overlay display. Maps to a command-line argument: -truncphaseflag 1.
snapshots : a list of items which are a pathlike object or string representing an existing file
Tiff images of the surface from different perspectives.

SurfaceTransform

Link to code

Bases: FSCommand

Wrapped executable: mri_surf2surf.

Transform a surface file from one subject to another via a spherical registration.

Both the source and target subject must reside in your Subjects Directory, and they must have been processed with recon-all, unless you are transforming to one of the icosahedron meshes.

Examples

>>> from nipype.interfaces.freesurfer import SurfaceTransform
>>> sxfm = SurfaceTransform()
>>> sxfm.inputs.source_file = "lh.cope1.nii.gz"
>>> sxfm.inputs.source_subject = "my_subject"
>>> sxfm.inputs.target_subject = "fsaverage"
>>> sxfm.inputs.hemi = "lh"
>>> sxfm.run() # doctest: +SKIP
hemi : ‘lh’ or ‘rh’
Hemisphere to transform. Maps to a command-line argument: --hemi %s.
source_annot_file : a pathlike object or string representing an existing file
Surface annotation file. Maps to a command-line argument: --sval-annot %s. Mutually exclusive with inputs: source_file.
source_file : a pathlike object or string representing an existing file
Surface file with source values. Maps to a command-line argument: --sval %s. Mutually exclusive with inputs: source_annot_file.
source_subject : a string
Subject id for source surface. Maps to a command-line argument: --srcsubject %s.
target_subject : a string
Subject id of target surface. Maps to a command-line argument: --trgsubject %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
out_file : a pathlike object or string representing a file
Surface file to write. Maps to a command-line argument: --tval %s.
reshape : a boolean
Reshape output surface to conform with Nifti. Maps to a command-line argument: --reshape.
reshape_factor : an integer (int or long)
Number of slices in reshaped image. Maps to a command-line argument: --reshape-factor.
source_type : ‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’
Source file format. Maps to a command-line argument: --sfmt %s. Requires inputs: source_file.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
target_ico_order : 1 or 2 or 3 or 4 or 5 or 6 or 7
Order of the icosahedron if target_subject is ‘ico’. Maps to a command-line argument: --trgicoorder %d.
target_type : ‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’ or ‘gii’
Output format. Maps to a command-line argument: --tfmt %s.
out_file : a pathlike object or string representing an existing file
Transformed surface file.

TalairachAVI

Link to code

Bases: FSCommand

Wrapped executable: talairach_avi.

Front-end for Avi Snyders image registration tool. Computes the talairach transform that maps the input volume to the MNI average_305. This does not add the xfm to the header of the input file. When called by recon-all, the xfm is added to the header after the transform is computed.

Examples

>>> from nipype.interfaces.freesurfer import TalairachAVI
>>> example = TalairachAVI()
>>> example.inputs.in_file = 'norm.mgz'
>>> example.inputs.out_file = 'trans.mat'
>>> example.cmdline
'talairach_avi --i norm.mgz --xfm trans.mat'

>>> example.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
Input volume. Maps to a command-line argument: --i %s.
out_file : a pathlike object or string representing a file
Output xfm file. Maps to a command-line argument: --xfm %s.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
atlas : a string
Alternate target atlas (in freesurfer/average dir). Maps to a command-line argument: --atlas %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
out_file : a pathlike object or string representing a file
The output transform for TalairachAVI.
out_log : a pathlike object or string representing a file
The output log file for TalairachAVI.
out_txt : a pathlike object or string representing a file
The output text file for TaliarachAVI.

TalairachQC

Link to code

Bases: FSScriptCommand

Wrapped executable: tal_QC_AZS.

Examples

>>> from nipype.interfaces.freesurfer import TalairachQC
>>> qc = TalairachQC()
>>> qc.inputs.log_file = 'dirs.txt'
>>> qc.cmdline
'tal_QC_AZS dirs.txt'
log_file : a pathlike object or string representing an existing file
The log file for TalairachQC. Maps to a command-line argument: %s (position: 0).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
log_file : a pathlike object or string representing an existing file
The output log. (Nipype default value: output.nipype)

Tkregister2

Link to code

Bases: FSCommand

Wrapped executable: tkregister2.

Examples

Get transform matrix between orig (tkRAS) and native (scannerRAS) coordinates in Freesurfer. Implements the first step of mapping surfaces to native space in this guide.

>>> from nipype.interfaces.freesurfer import Tkregister2
>>> tk2 = Tkregister2(reg_file='T1_to_native.dat')
>>> tk2.inputs.moving_image = 'T1.mgz'
>>> tk2.inputs.target_image = 'structural.nii'
>>> tk2.inputs.reg_header = True
>>> tk2.cmdline
'tkregister2 --mov T1.mgz --noedit --reg T1_to_native.dat --regheader --targ structural.nii'
>>> tk2.run() # doctest: +SKIP

The example below uses tkregister2 without the manual editing stage to convert FSL-style registration matrix (.mat) to FreeSurfer-style registration matrix (.dat)

>>> from nipype.interfaces.freesurfer import Tkregister2
>>> tk2 = Tkregister2()
>>> tk2.inputs.moving_image = 'epi.nii'
>>> tk2.inputs.fsl_in_matrix = 'flirt.mat'
>>> tk2.cmdline
'tkregister2 --fsl flirt.mat --mov epi.nii --noedit --reg register.dat'
>>> tk2.run() # doctest: +SKIP
moving_image : a pathlike object or string representing an existing file
Moving volume. Maps to a command-line argument: --mov %s.
reg_file : a pathlike object or string representing a file
Freesurfer-style registration file. Maps to a command-line argument: --reg %s. (Nipype default value: register.dat)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
fsl_in_matrix : a pathlike object or string representing an existing file
Fsl-style registration input matrix. Maps to a command-line argument: --fsl %s.
fsl_out : a bool or None or a pathlike object or string representing a file
Compute an FSL-compatible resgitration matrix. Maps to a command-line argument: --fslregout %s.
fstal : a boolean
Set mov to be tal and reg to be tal xfm. Maps to a command-line argument: --fstal. Mutually exclusive with inputs: target_image, moving_image, reg_file.
fstarg : a boolean
Use subject’s T1 as reference. Maps to a command-line argument: --fstarg. Mutually exclusive with inputs: target_image.
invert_lta_in : a boolean
Invert input LTA before applying. Requires inputs: lta_in.
invert_lta_out : a boolean
Invert input LTA before applying. Maps to a command-line argument: --ltaout-inv. Requires inputs: lta_in.
lta_in : a pathlike object or string representing an existing file
Use a matrix in MNI coordinates as initial registration. Maps to a command-line argument: --lta %s.
lta_out : a bool or None or a pathlike object or string representing a file
Output registration file (LTA format). Maps to a command-line argument: --ltaout %s.
movscale : a float
Adjust registration matrix to scale mov. Maps to a command-line argument: --movscale %f.
noedit : a boolean
Do not open edit window (exit). Maps to a command-line argument: --noedit. (Nipype default value: True)
reg_header : a boolean
Compute regstration from headers. Maps to a command-line argument: --regheader.
subject_id : a string
Freesurfer subject ID. Maps to a command-line argument: --s %s.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
target_image : a pathlike object or string representing an existing file
Target volume. Maps to a command-line argument: --targ %s. Mutually exclusive with inputs: fstarg.
xfm : a pathlike object or string representing an existing file
Use a matrix in MNI coordinates as initial registration. Maps to a command-line argument: --xfm %s.
fsl_file : a pathlike object or string representing a file
FSL-style registration file.
lta_file : a pathlike object or string representing a file
LTA-style registration file.
reg_file : a pathlike object or string representing an existing file
Freesurfer-style registration file.

VolumeMask

Link to code

Bases: FSCommand

Wrapped executable: mris_volmask.

Computes a volume mask, at the same resolution as the <subject>/mri/brain.mgz. The volume mask contains 4 values: LH_WM (default 10), LH_GM (default 100), RH_WM (default 20), RH_GM (default 200). The algorithm uses the 4 surfaces situated in <subject>/surf/ [lh|rh].[white|pial] and labels voxels based on the signed-distance function from the surface.

Examples

>>> from nipype.interfaces.freesurfer import VolumeMask
>>> volmask = VolumeMask()
>>> volmask.inputs.left_whitelabel = 2
>>> volmask.inputs.left_ribbonlabel = 3
>>> volmask.inputs.right_whitelabel = 41
>>> volmask.inputs.right_ribbonlabel = 42
>>> volmask.inputs.lh_pial = 'lh.pial'
>>> volmask.inputs.rh_pial = 'lh.pial'
>>> volmask.inputs.lh_white = 'lh.pial'
>>> volmask.inputs.rh_white = 'lh.pial'
>>> volmask.inputs.subject_id = '10335'
>>> volmask.inputs.save_ribbon = True
>>> volmask.cmdline
'mris_volmask --label_left_ribbon 3 --label_left_white 2 --label_right_ribbon 42 --label_right_white 41 --save_ribbon 10335'
left_ribbonlabel : an integer (int or long)
Left cortical ribbon label. Maps to a command-line argument: --label_left_ribbon %d.
left_whitelabel : an integer (int or long)
Left white matter label. Maps to a command-line argument: --label_left_white %d.
lh_pial : a pathlike object or string representing an existing file
Implicit input left pial surface.
lh_white : a pathlike object or string representing an existing file
Implicit input left white matter surface.
rh_pial : a pathlike object or string representing an existing file
Implicit input right pial surface.
rh_white : a pathlike object or string representing an existing file
Implicit input right white matter surface.
right_ribbonlabel : an integer (int or long)
Right cortical ribbon label. Maps to a command-line argument: --label_right_ribbon %d.
right_whitelabel : an integer (int or long)
Right white matter label. Maps to a command-line argument: --label_right_white %d.
subject_id : a string
Subject being processed. Maps to a command-line argument: %s (position: -1). (Nipype default value: subject_id)
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
aseg : a pathlike object or string representing an existing file
Implicit aseg.mgz segmentation. Specify a different aseg by using the ‘in_aseg’ input. Mutually exclusive with inputs: in_aseg.
copy_inputs : a boolean
If running as a node, set this to True.This will copy the implicit input files to the node directory.
environ : a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’
Environment variables. (Nipype default value: {})
in_aseg : a pathlike object or string representing an existing file
Input aseg file for VolumeMask. Maps to a command-line argument: --aseg_name %s. Mutually exclusive with inputs: aseg.
save_ribbon : a boolean
Option to save just the ribbon for the hemispheres in the format ?h.ribbon.mgz. Maps to a command-line argument: --save_ribbon.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
lh_ribbon : a pathlike object or string representing a file
Output left cortical ribbon mask.
out_ribbon : a pathlike object or string representing a file
Output cortical ribbon mask.
rh_ribbon : a pathlike object or string representing a file
Output right cortical ribbon mask.
VolumeMask.run(**inputs)

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:
  • cwd (specify a folder where the interface should be run) –
  • inputs (allows the interface settings to be updated) –
Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results
Return type:

nipype.interfaces.base.support.InterfaceResult
nipype.interfaces.freesurfer.utils.copy2subjdir(cls, in_file, folder=None, basename=None, subject_id=None)

Method to copy an input to the subjects directory

nipype.interfaces.freesurfer.utils.createoutputdirs(outputs)

create all output directories. If not created, some freesurfer interfaces fail