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 transform 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'
Mandatory Inputs:

  • 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).

Optional Inputs:

  • args (a 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) – Align to atlas containing skull setting unknown_nbr_spacing = nbrspacing. Maps to a command-line argument: -uns %d.

  • num_threads (an integer) – 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.

Outputs:

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 = '.' 
>>> mprtomni305.cmdline 
'mpr2mni305 output'
>>> mprtomni305.inputs.out_file = 'struct_out' 
>>> mprtomni305.cmdline 
'mpr2mni305 struct_out' 
>>> mprtomni305.inputs.environ['REFDIR'] == os.path.join(Info.home(), 'average') 
True
>>> mprtomni305.inputs.environ['MPR2MNI305_TARGET'] 
'structural'
>>> mprtomni305.run()
Mandatory Inputs:

  • reference_dir (a pathlike object or string representing an existing directory) – TODO. (Nipype default value: "")

  • target (a string) – Input atlas file. (Nipype default value: "")

Optional Inputs:

  • args (a 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.

Outputs:

  • 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 
'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 
'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 
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --mov moving1.nii --sd .'

>>> coreg.inputs.sep = [4, 5]
>>> coreg.cmdline 
'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --sep 5 --mov moving1.nii --sd .'
Mandatory Inputs:

  • 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 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.

Optional Inputs:

  • args (a 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) – 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 (an 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) – 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 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 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.

Outputs:

  • 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'
Mandatory Inputs:

  • 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).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • averages (an integer) – 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) – Frame number of the input template.

Outputs:

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'
Mandatory Inputs:

  • 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).

Optional Inputs:

  • args (a 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.

Outputs:

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'                         
>>> register.inputs.target = 'mni305.cor.mgz'                          
>>> register.inputs.vox2vox = 'talsrcimg_to_structural_t4_vox2vox.txt' 
>>> register.cmdline                                                   
'avi2talxfm structural.mgz mni305.cor.mgz talsrcimg_to_structural_t4_vox2vox.txt talairach.auto.xfm'

>>> register.run()
Mandatory Inputs:

  • 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).

Optional Inputs:

  • args (a 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.

Outputs:

  • 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.