nipype.interfaces.freesurfer.registration module

Provides interfaces to various longitudinal commands provided by freesurfer

EMRegister

Link to code

Bases: FSCommandOpenMP

Wrapped executable: mri_em_register.

This program creates a tranform in lta format

Examples

>>> from nipype.interfaces.freesurfer import EMRegister
>>> register = EMRegister()
>>> register.inputs.in_file = 'norm.mgz'
>>> register.inputs.template = 'aseg.mgz'
>>> register.inputs.out_file = 'norm_transform.lta'
>>> register.inputs.skull = True
>>> register.inputs.nbrspacing = 9
>>> register.cmdline
'mri_em_register -uns 9 -skull norm.mgz aseg.mgz norm_transform.lta'
in_file : a pathlike object or string representing an existing file
In brain volume. Maps to a command-line argument: %s (position: -3).
template : a pathlike object or string representing an existing file
Template gca. 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: {})
mask : a pathlike object or string representing an existing file
Use volume as a mask. Maps to a command-line argument: -mask %s.
nbrspacing : an integer (int or long)
Align to atlas containing skull setting unknown_nbr_spacing = nbrspacing. Maps to a command-line argument: -uns %d.
num_threads : an integer (int or long)
Allows for specifying more threads.
out_file : a pathlike object or string representing a file
Output transform. Maps to a command-line argument: %s (position: -1).
skull : a boolean
Align to atlas containing skull (uns=5). Maps to a command-line argument: -skull.
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
transform : a pathlike object or string representing an existing file
Previously computed transform. Maps to a command-line argument: -t %s.
out_file : a pathlike object or string representing a file
Output transform.

MPRtoMNI305

Link to code

Bases: FSScriptCommand

Wrapped executable: mpr2mni305.

For complete details, see FreeSurfer documentation

Examples

>>> from nipype.interfaces.freesurfer import MPRtoMNI305, Info
>>> mprtomni305 = MPRtoMNI305()
>>> mprtomni305.inputs.target = 'structural.nii'
>>> mprtomni305.inputs.reference_dir = '.' # doctest: +SKIP
>>> mprtomni305.cmdline # doctest: +SKIP
'mpr2mni305 output'
>>> mprtomni305.inputs.out_file = 'struct_out' # doctest: +SKIP
>>> mprtomni305.cmdline # doctest: +SKIP
'mpr2mni305 struct_out' # doctest: +SKIP
>>> mprtomni305.inputs.environ['REFDIR'] == os.path.join(Info.home(), 'average') # doctest: +SKIP
True
>>> mprtomni305.inputs.environ['MPR2MNI305_TARGET'] # doctest: +SKIP
'structural'
>>> mprtomni305.run() # doctest: +SKIP
reference_dir : a pathlike object or string representing an existing directory
TODO. (Nipype default value: "")
target : a string
Input atlas file. (Nipype default value: "")
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 a file
The input file prefix for MPRtoMNI305. Maps to a command-line argument: %s. (Nipype default value: <undefined>)
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)
out_file : a pathlike object or string representing a file
The output file ‘<in_file>_to_<target>_t4_vox2vox.txt’.

MRICoreg

Link to code

Bases: FSCommand

Wrapped executable: mri_coreg.

This program registers one volume to another

mri_coreg is a C reimplementation of spm_coreg in FreeSurfer

Examples

>>> from nipype.interfaces.freesurfer import MRICoreg
>>> coreg = MRICoreg()
>>> coreg.inputs.source_file = 'moving1.nii'
>>> coreg.inputs.reference_file = 'fixed1.nii'
>>> coreg.inputs.subjects_dir = '.'
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --lta .../registration.lta --ref fixed1.nii --mov moving1.nii --sd .'

If passing a subject ID, the reference mask may be disabled:

>>> coreg = MRICoreg()
>>> coreg.inputs.source_file = 'moving1.nii'
>>> coreg.inputs.subjects_dir = '.'
>>> coreg.inputs.subject_id = 'fsaverage'
>>> coreg.inputs.reference_mask = False
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --mov moving1.nii --sd .'

Spatial scales may be specified as a list of one or two separations:

>>> coreg.inputs.sep = [4]
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --mov moving1.nii --sd .'

>>> coreg.inputs.sep = [4, 5]
>>> coreg.cmdline # doctest: +ELLIPSIS
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --sep 5 --mov moving1.nii --sd .'
reference_file : a pathlike object or string representing a file
Reference (target) file. Maps to a command-line argument: --ref %s. Mutually exclusive with inputs: subject_id.
source_file : a pathlike object or string representing a file
Source file to be registered. Maps to a command-line argument: --mov %s.
subject_id : a unicode string
Freesurfer subject ID (implies reference_mask == aparc+aseg.mgz unless otherwise specified). Maps to a command-line argument: --s %s (position: 1). Mutually exclusive with inputs: reference_file. Requires inputs: subjects_dir.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
brute_force_limit : a float
Constrain brute force search to +/- lim. Maps to a command-line argument: --bf-lim %g. Mutually exclusive with inputs: no_brute_force.
brute_force_samples : an integer (int or long)
Number of samples in brute force search. Maps to a command-line argument: --bf-nsamp %d. Mutually exclusive with inputs: no_brute_force.
conform_reference : a boolean
Conform reference without rescaling. Maps to a command-line argument: --conf-ref.
dof : 6 or 9 or 12
Number of transform degrees of freedom. Maps to a command-line argument: --dof %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: {})
ftol : a float
Floating-point tolerance (default=1e-7). Maps to a command-line argument: --ftol %e.
initial_rotation : a tuple of the form: (a float, a float, a float)
Initial rotation in degrees. Maps to a command-line argument: --rot %g %g %g.
initial_scale : a tuple of the form: (a float, a float, a float)
Initial scale. Maps to a command-line argument: --scale %g %g %g.
initial_shear : a tuple of the form: (a float, a float, a float)
Initial shear (Hxy, Hxz, Hyz). Maps to a command-line argument: --shear %g %g %g.
initial_translation : a tuple of the form: (a float, a float, a float)
Initial translation in mm (implies no_cras0). Maps to a command-line argument: --trans %g %g %g.
linmintol : a float
Maps to a command-line argument: --linmintol %e.
max_iters : a long integer >= 1
Maximum iterations (default: 4). Maps to a command-line argument: --nitersmax %d.
no_brute_force : a boolean
Do not brute force search. Maps to a command-line argument: --no-bf.
no_coord_dithering : a boolean
Turn off coordinate dithering. Maps to a command-line argument: --no-coord-dither.
no_cras0 : a boolean
Do not set translation parameters to align centers of source and reference files. Maps to a command-line argument: --no-cras0.
no_intensity_dithering : a boolean
Turn off intensity dithering. Maps to a command-line argument: --no-intensity-dither.
no_smooth : a boolean
Do not apply smoothing to either reference or source file. Maps to a command-line argument: --no-smooth.
num_threads : an integer (int or long)
Number of OpenMP threads. Maps to a command-line argument: --threads %d.
out_lta_file : a bool or None or a pathlike object or string representing a file
Output registration file (LTA format). Maps to a command-line argument: --lta %s. (Nipype default value: True)
out_params_file : a bool or None or a pathlike object or string representing a file
Output parameters file. Maps to a command-line argument: --params %s.
out_reg_file : a bool or None or a pathlike object or string representing a file
Output registration file (REG format). Maps to a command-line argument: --regdat %s.
ref_fwhm : a float
Apply smoothing to reference file. Maps to a command-line argument: --ref-fwhm.
reference_mask : a bool or None or a unicode string
Mask reference volume with given mask, or None if False. Maps to a command-line argument: --ref-mask %s (position: 2).
saturation_threshold : 0.0 <= a floating point number <= 100.0
Saturation threshold (default=9.999). Maps to a command-line argument: --sat %g.
sep : a list of from 1 to 2 items which are any value
Set spatial scales, in voxels (default [2, 4]). Maps to a command-line argument: --sep %s....
source_mask : a unicode string
Mask source file with given mask. Maps to a command-line argument: --mov-mask.
source_oob : a boolean
Count source voxels that are out-of-bounds as 0. Maps to a command-line argument: --mov-oob.
subjects_dir : a pathlike object or string representing an existing directory
FreeSurfer SUBJECTS_DIR. Maps to a command-line argument: --sd %s.
out_lta_file : a pathlike object or string representing an existing file
Output LTA-style registration file.
out_params_file : a pathlike object or string representing an existing file
Output parameters file.
out_reg_file : a pathlike object or string representing an existing file
Output registration file.

Paint

Link to code

Bases: FSCommand

Wrapped executable: mrisp_paint.

This program is useful for extracting one of the arrays (“a variable”) from a surface-registration template file. The output is a file containing a surface-worth of per-vertex values, saved in “curvature” format. Because the template data is sampled to a particular surface mesh, this conjures the idea of “painting to a surface”.

Examples

>>> from nipype.interfaces.freesurfer import Paint
>>> paint = Paint()
>>> paint.inputs.in_surf = 'lh.pial'
>>> paint.inputs.template = 'aseg.mgz'
>>> paint.inputs.averages = 5
>>> paint.inputs.out_file = 'lh.avg_curv'
>>> paint.cmdline
'mrisp_paint -a 5 aseg.mgz lh.pial lh.avg_curv'
in_surf : a pathlike object or string representing an existing file
Surface file with grid (vertices) onto which the template data is to be sampled or ‘painted’. Maps to a command-line argument: %s (position: -2).
template : a pathlike object or string representing an existing file
Template 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.
averages : an integer (int or long)
Average curvature patterns. Maps to a command-line argument: -a %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: {})
out_file : a pathlike object or string representing a file
File containing a surface-worth of per-vertex values, saved in ‘curvature’ format. Maps to a command-line argument: %s (position: -1).
subjects_dir : a pathlike object or string representing an existing directory
Subjects directory.
template_param : an integer (int or long)
Frame number of the input template.
out_file : a pathlike object or string representing a file
File containing a surface-worth of per-vertex values, saved in ‘curvature’ format.

Register

Link to code

Bases: FSCommand

Wrapped executable: mris_register.

This program registers a surface to an average surface template.

Examples

>>> from nipype.interfaces.freesurfer import Register
>>> register = Register()
>>> register.inputs.in_surf = 'lh.pial'
>>> register.inputs.in_smoothwm = 'lh.pial'
>>> register.inputs.in_sulc = 'lh.pial'
>>> register.inputs.target = 'aseg.mgz'
>>> register.inputs.out_file = 'lh.pial.reg'
>>> register.inputs.curv = True
>>> register.cmdline
'mris_register -curv lh.pial aseg.mgz lh.pial.reg'
in_sulc : a pathlike object or string representing an existing file
Undocumented mandatory input file ${SUBJECTS_DIR}/surf/{hemisphere}.sulc .
in_surf : a pathlike object or string representing an existing file
Surface to register, often {hemi}.sphere. Maps to a command-line argument: %s (position: -3).
target : a pathlike object or string representing an existing file
The data to register to. In normal recon-all usage, this is a template file for average surface. 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.
curv : a boolean
Use smoothwm curvature for final alignment. Maps to a command-line argument: -curv. Requires inputs: in_smoothwm.
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
Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm .
out_file : a pathlike object or string representing a file
Output surface file to capture registration. 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 surface file to capture registration.

RegisterAVItoTalairach

Link to code

Bases: FSScriptCommand

Wrapped executable: avi2talxfm.

converts the vox2vox from talairach_avi to a talairach.xfm file

This is a script that converts the vox2vox from talairach_avi to a talairach.xfm file. It is meant to replace the following cmd line:

tkregister2_cmdl –mov $InVol –targ $FREESURFER_HOME/average/mni305.cor.mgz –xfmout ${XFM} –vox2vox talsrcimg_to_${target}_t4_vox2vox.txt –noedit –reg talsrcimg.reg.tmp.dat set targ = $FREESURFER_HOME/average/mni305.cor.mgz set subject = mgh-02407836-v2 set InVol = $SUBJECTS_DIR/$subject/mri/orig.mgz set vox2vox = $SUBJECTS_DIR/$subject/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt

Examples

>>> from nipype.interfaces.freesurfer import RegisterAVItoTalairach
>>> register = RegisterAVItoTalairach()
>>> register.inputs.in_file = 'structural.mgz'                         # doctest: +SKIP
>>> register.inputs.target = 'mni305.cor.mgz'                          # doctest: +SKIP
>>> register.inputs.vox2vox = 'talsrcimg_to_structural_t4_vox2vox.txt' # doctest: +SKIP
>>> register.cmdline                                                   # doctest: +SKIP
'avi2talxfm structural.mgz mni305.cor.mgz talsrcimg_to_structural_t4_vox2vox.txt talairach.auto.xfm'

>>> register.run() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
The input file. Maps to a command-line argument: %s (position: 0).
target : a pathlike object or string representing an existing file
The target file. Maps to a command-line argument: %s (position: 1).
vox2vox : a pathlike object or string representing an existing file
The vox2vox file. 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
The transform output. Maps to a command-line argument: %s (position: 3). (Nipype default value: talairach.auto.xfm)
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)
out_file : a pathlike object or string representing a file
The output file for RegisterAVItoTalairach.