interfaces.freesurfer.registration¶
EMRegister¶
Wraps the executable command 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'
Inputs:
[Mandatory]
in_file: (an existing file name)
in brain volume
argument: ``%s``, position: -3
template: (an existing file name)
template gca
argument: ``%s``, position: -2
[Optional]
out_file: (a file name)
output transform
argument: ``%s``, position: -1
skull: (a boolean)
align to atlas containing skull (uns=5)
argument: ``-skull``
mask: (an existing file name)
use volume as a mask
argument: ``-mask %s``
nbrspacing: (an integer (int or long))
align to atlas containing skull setting unknown_nbr_spacing =
nbrspacing
argument: ``-uns %d``
transform: (an existing file name)
Previously computed transform
argument: ``-t %s``
num_threads: (an integer (int or long))
allows for specifying more threads
subjects_dir: (an existing directory name)
subjects directory
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a file name)
output transform
MPRtoMNI305¶
Wraps the executable command 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()
Inputs:
[Mandatory]
reference_dir: (an existing directory name, nipype default value: )
TODO
target: (a string, nipype default value: )
input atlas file
[Optional]
in_file: (a file name, nipype default value: )
the input file prefix for MPRtoMNI305
argument: ``%s``
subjects_dir: (an existing directory name)
subjects directory
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a file name)
The output file '<in_file>_to_<target>_t4_vox2vox.txt'
log_file: (an existing file name, nipype default value:
output.nipype)
The output log
MRICoreg¶
Wraps the executable command 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 .'
Inputs:
[Mandatory]
source_file: (a file name)
source file to be registered
argument: ``--mov %s``
reference_file: (a file name)
reference (target) file
argument: ``--ref %s``
mutually_exclusive: subject_id
subject_id: (a unicode string)
freesurfer subject ID (implies ``reference_mask == aparc+aseg.mgz``
unless otherwise specified)
argument: ``--s %s``, position: 1
mutually_exclusive: reference_file
requires: subjects_dir
[Optional]
out_lta_file: (a bool or None or a file name, nipype default value:
True)
output registration file (LTA format)
argument: ``--lta %s``
out_reg_file: (a bool or None or a file name)
output registration file (REG format)
argument: ``--regdat %s``
out_params_file: (a bool or None or a file name)
output parameters file
argument: ``--params %s``
subjects_dir: (an existing directory name)
FreeSurfer SUBJECTS_DIR
argument: ``--sd %s``
dof: (6 or 9 or 12)
number of transform degrees of freedom
argument: ``--dof %d``
reference_mask: (a bool or None or a unicode string)
mask reference volume with given mask, or None if ``False``
argument: ``--ref-mask %s``, position: 2
source_mask: (a unicode string)
mask source file with given mask
argument: ``--mov-mask``
num_threads: (an integer (int or long))
number of OpenMP threads
argument: ``--threads %d``
no_coord_dithering: (a boolean)
turn off coordinate dithering
argument: ``--no-coord-dither``
no_intensity_dithering: (a boolean)
turn off intensity dithering
argument: ``--no-intensity-dither``
sep: (a list of from 1 to 2 items which are any value)
set spatial scales, in voxels (default [2, 4])
argument: ``--sep %s...``
initial_translation: (a tuple of the form: (a float, a float, a
float))
initial translation in mm (implies no_cras0)
argument: ``--trans %g %g %g``
initial_rotation: (a tuple of the form: (a float, a float, a float))
initial rotation in degrees
argument: ``--rot %g %g %g``
initial_scale: (a tuple of the form: (a float, a float, a float))
initial scale
argument: ``--scale %g %g %g``
initial_shear: (a tuple of the form: (a float, a float, a float))
initial shear (Hxy, Hxz, Hyz)
argument: ``--shear %g %g %g``
no_cras0: (a boolean)
do not set translation parameters to align centers of source and
reference files
argument: ``--no-cras0``
max_iters: (a long integer >= 1)
maximum iterations (default: 4)
argument: ``--nitersmax %d``
ftol: (a float)
floating-point tolerance (default=1e-7)
argument: ``--ftol %e``
linmintol: (a float)
argument: ``--linmintol %e``
saturation_threshold: (0.0 <= a floating point number <= 100.0)
saturation threshold (default=9.999)
argument: ``--sat %g``
conform_reference: (a boolean)
conform reference without rescaling
argument: ``--conf-ref``
no_brute_force: (a boolean)
do not brute force search
argument: ``--no-bf``
brute_force_limit: (a float)
constrain brute force search to +/- lim
argument: ``--bf-lim %g``
mutually_exclusive: no_brute_force
brute_force_samples: (an integer (int or long))
number of samples in brute force search
argument: ``--bf-nsamp %d``
mutually_exclusive: no_brute_force
no_smooth: (a boolean)
do not apply smoothing to either reference or source file
argument: ``--no-smooth``
ref_fwhm: (a float)
apply smoothing to reference file
argument: ``--ref-fwhm``
source_oob: (a boolean)
count source voxels that are out-of-bounds as 0
argument: ``--mov-oob``
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_reg_file: (an existing file name)
output registration file
out_lta_file: (an existing file name)
output LTA-style registration file
out_params_file: (an existing file name)
output parameters file
Paint¶
Wraps the executable command 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'
Inputs:
[Mandatory]
in_surf: (an existing file name)
Surface file with grid (vertices) onto which the template data is to
be sampled or 'painted'
argument: ``%s``, position: -2
template: (an existing file name)
Template file
argument: ``%s``, position: -3
[Optional]
template_param: (an integer (int or long))
Frame number of the input template
averages: (an integer (int or long))
Average curvature patterns
argument: ``-a %d``
out_file: (a file name)
File containing a surface-worth of per-vertex values, saved in
'curvature' format.
argument: ``%s``, position: -1
subjects_dir: (an existing directory name)
subjects directory
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a file name)
File containing a surface-worth of per-vertex values, saved in
'curvature' format.
Register¶
Wraps the executable command 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'
Inputs:
[Mandatory]
in_surf: (an existing file name)
Surface to register, often {hemi}.sphere
argument: ``%s``, position: -3
target: (an existing file name)
The data to register to. In normal recon-all usage, this is a
template file for average surface.
argument: ``%s``, position: -2
in_sulc: (an existing file name)
Undocumented mandatory input file
${SUBJECTS_DIR}/surf/{hemisphere}.sulc
[Optional]
out_file: (a file name)
Output surface file to capture registration
argument: ``%s``, position: -1
curv: (a boolean)
Use smoothwm curvature for final alignment
argument: ``-curv``
requires: in_smoothwm
in_smoothwm: (an existing file name)
Undocumented input file ${SUBJECTS_DIR}/surf/{hemisphere}.smoothwm
subjects_dir: (an existing directory name)
subjects directory
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a file name)
Output surface file to capture registration
RegisterAVItoTalairach¶
Wraps the executable command 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()
Inputs:
[Mandatory]
in_file: (an existing file name)
The input file
argument: ``%s``, position: 0
target: (an existing file name)
The target file
argument: ``%s``, position: 1
vox2vox: (an existing file name)
The vox2vox file
argument: ``%s``, position: 2
[Optional]
out_file: (a file name, nipype default value: talairach.auto.xfm)
The transform output
argument: ``%s``, position: 3
subjects_dir: (an existing directory name)
subjects directory
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a file name)
The output file for RegisterAVItoTalairach
log_file: (an existing file name, nipype default value:
output.nipype)
The output log