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# 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'

> in_filea pathlike object or string representing an existing file

>   In brain volume. Maps to a command-line argument: `%s` (position: -3).

> templatea pathlike object or string representing an existing file

>   Template gca. Maps to a command-line argument: `%s` (position: -2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa 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: `{}`)

> maska pathlike object or string representing an existing file

>   Use volume as a mask. Maps to a command-line argument: `-mask %s`.

> nbrspacingan integer

>   Align to atlas containing skull setting unknown_nbr_spacing = nbrspacing. Maps to a command-line argument: `-uns %d`.

> num_threadsan integer

>   Allows for specifying more threads.

> out_filea pathlike object or string representing a file

>   Output transform. Maps to a command-line argument: `%s` (position: -1).

> skulla boolean

>   Align to atlas containing skull (uns=5). Maps to a command-line argument: `-skull`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> transforma pathlike object or string representing an existing file

>   Previously computed transform. Maps to a command-line argument: `-t %s`.

> out_filea 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()

> reference_dira pathlike object or string representing an existing directory

>   TODO. (Nipype default value: `""`)

> targeta string

>   Input atlas file. (Nipype default value: `""`)

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa 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_filea 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_dira pathlike object or string representing an existing directory

>   Subjects directory.

> log_filea pathlike object or string representing an existing file

>   The output log. (Nipype default value: `output.nipype`)

> out_filea 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 .'

> reference_filea 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_filea pathlike object or string representing a file

>   Source file to be registered. Maps to a command-line argument: `--mov %s`.

> subject_ida 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`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> brute_force_limita 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_samplesan 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_referencea boolean

>   Conform reference without rescaling. Maps to a command-line argument: `--conf-ref`.

> dof6 or 9 or 12

>   Number of transform degrees of freedom. Maps to a command-line argument: `--dof %d`.

> environa 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: `{}`)

> ftola float

>   Floating-point tolerance (default=1e-7). Maps to a command-line argument: `--ftol %e`.

> initial_rotationa 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_scalea tuple of the form: (a float, a float, a float)

>   Initial scale. Maps to a command-line argument: `--scale %g %g %g`.

> initial_sheara 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_translationa 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`.

> linmintola float

>   Maps to a command-line argument: `--linmintol %e`.

> max_itersan integer >= 1

>   Maximum iterations (default: 4). Maps to a command-line argument: `--nitersmax %d`.

> no_brute_forcea boolean

>   Do not brute force search. Maps to a command-line argument: `--no-bf`.

> no_coord_ditheringa boolean

>   Turn off coordinate dithering. Maps to a command-line argument: `--no-coord-dither`.

> no_cras0a boolean

>   Do not set translation parameters to align centers of source and reference files. Maps to a command-line argument: `--no-cras0`.

> no_intensity_ditheringa boolean

>   Turn off intensity dithering. Maps to a command-line argument: `--no-intensity-dither`.

> no_smootha boolean

>   Do not apply smoothing to either reference or source file. Maps to a command-line argument: `--no-smooth`.

> num_threadsan integer

>   Number of OpenMP threads. Maps to a command-line argument: `--threads %d`.

> out_lta_filea 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_filea 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_filea 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_fwhma float

>   Apply smoothing to reference file. Maps to a command-line argument: `--ref-fwhm`.

> reference_maska 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_threshold0.0 <= a floating point number <= 100.0

>   Saturation threshold (default=9.999). Maps to a command-line argument: `--sat %g`.

> sepa 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_maska string

>   Mask source file with given mask. Maps to a command-line argument: `--mov-mask`.

> source_ooba boolean

>   Count source voxels that are out-of-bounds as 0. Maps to a command-line argument: `--mov-oob`.

> subjects_dira pathlike object or string representing an existing directory

>   FreeSurfer SUBJECTS_DIR. Maps to a command-line argument: `--sd %s`.

> out_lta_filea pathlike object or string representing an existing file

>   Output LTA-style registration file.

> out_params_filea pathlike object or string representing an existing file

>   Output parameters file.

> out_reg_filea 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_surfa 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).

> templatea pathlike object or string representing an existing file

>   Template file. Maps to a command-line argument: `%s` (position: -3).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> averagesan integer

>   Average curvature patterns. Maps to a command-line argument: `-a %d`.

> environa 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_filea 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_dira pathlike object or string representing an existing directory

>   Subjects directory.

> template_paraman integer

>   Frame number of the input template.

> out_filea 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_sulca pathlike object or string representing an existing file

>   Undocumented mandatory input file ${SUBJECTS_DIR}/surf/{hemisphere}.sulc .

> in_surfa pathlike object or string representing an existing file

>   Surface to register, often {hemi}.sphere. Maps to a command-line argument: `%s` (position: -3).

> targeta 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).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> curva boolean

>   Use smoothwm curvature for final alignment. Maps to a command-line argument: `-curv`. Requires inputs: `in_smoothwm`.

> environa 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_smoothwma pathlike object or string representing an existing file

>   Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm .

> out_filea pathlike object or string representing a file

>   Output surface file to capture registration. Maps to a command-line argument: `%s` (position: -1).

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> out_filea 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()

> in_filea pathlike object or string representing an existing file

>   The input file. Maps to a command-line argument: `%s` (position: 0).

> targeta pathlike object or string representing an existing file

>   The target file. Maps to a command-line argument: `%s` (position: 1).

> vox2voxa pathlike object or string representing an existing file

>   The vox2vox file. Maps to a command-line argument: `%s` (position: 2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa 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_filea 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_dira pathlike object or string representing an existing directory

>   Subjects directory.

> log_filea pathlike object or string representing an existing file

>   The output log. (Nipype default value: `output.nipype`)

> out_filea pathlike object or string representing a file

>   The output file for RegisterAVItoTalairach.