cmtklib.interfaces.freesurfer module

The FreeSurfer module provides Nipype interfaces for Freesurfer tools missing in nipype or modified.

BBRegister

Link to code

Bases: nipype.interfaces.freesurfer.base.FSCommand

Wrapped executable: bbregister.

Use FreeSurfer bbregister to register a volume to the Freesurfer anatomical.

This program performs within-subject, cross-modal registration using a

boundary-based cost function. The registration is constrained to be 6 DOF (rigid).

It is required that you have an anatomical scan of the subject that has

already been recon-all-ed using freesurfer.

Examples

>>> from cmtklib.interfaces.freesurfer import BBRegister
>>> bbreg = BBRegister(subject_id='me',
>>>                    source_file='structural.nii',
>>>                    init='header',
>>>                    contrast_type='t2')
>>> bbreg.run()  
contrast_type‘t1’ or ‘t2’ or ‘dti’

Contrast type of image. Maps to a command-line argument: --%s.

init‘spm’ or ‘fsl’ or ‘header’

Initialize registration spm, fsl, header. Maps to a command-line argument: --init-%s. Mutually exclusive with inputs: init_reg_file.

init_reg_filea pathlike object or string representing an existing file

Existing registration file. Mutually exclusive with inputs: init.

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. Maps to a command-line argument: --s %s.

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: {})

epi_maska boolean

Mask out B0 regions in stages 1 and 2. Maps to a command-line argument: --epi-mask.

intermediate_filea pathlike object or string representing an existing file

Intermediate image, e.g. in case of partial FOV. Maps to a command-line argument: --int %s.

out_fsl_filea boolean or a pathlike object or string representing a file

Write the transformation matrix in FSL FLIRT format. Maps to a command-line argument: --fslmat %s.

out_reg_filea pathlike object or string representing a file

Output registration file. Maps to a command-line argument: --reg %s.

reg_framean integer

0-based frame index for 4D source file. Maps to a command-line argument: --frame %d. Mutually exclusive with inputs: reg_middle_frame.

reg_middle_framea boolean

Register middle frame of 4D source file. Maps to a command-line argument: --mid-frame. Mutually exclusive with inputs: reg_frame.

registered_filea boolean or a pathlike object or string representing a file

Output warped sourcefile either True or filename. Maps to a command-line argument: --o %s.

spm_niftia boolean

Force use of nifti rather than analyze with SPM. Maps to a command-line argument: --spm-nii.

subjects_dira pathlike object or string representing an existing directory

Subjects directory.

min_cost_filea pathlike object or string representing an existing file

Output registration minimum cost file.

out_fsl_filea pathlike object or string representing a file

Output FLIRT-style registration file.

out_reg_filea pathlike object or string representing an existing file

Output registration file.

registered_filea pathlike object or string representing a file

Registered and resampled source file.

Tkregister2

Link to code

Bases: nipype.interfaces.base.core.CommandLine

Wrapped executable: tkregister2.

Performs image co-registration using Freesurfer tkregister2.

Examples

>>> from cmtklib.interfaces.freesurfer import Tkregister2
>>> tkreg = Tkregister2()
>>> tkreg.inputs.in_file = 'sub-01_desc-brain_mask.nii.gz'
>>> tkreg.inputs.subject_dir = '/path/to/output_dir/freesurfer/sub-01'
>>> tkreg.inputs.subjects_dir = '/path/to/output_dir/freesurfer'
>>> tkreg.inputs.subject_id = 'sub-01'
>>> tkreg.inputs.regheader = True
>>> tkreg.inputs.in_file = '/path/to/moving_image.nii.gz'
>>> tkreg.inputs.target_file = '/path/to/fixed_image.nii.gz'
>>> tkreg.inputs.fslreg_out = 'motions.par'
>>> tkreg.inputs.noedit = True
>>> tkreg.run()  
fslreg_outa string

FSL-Style registration output matrix. Maps to a command-line argument: --fslregout %s.

in_filea pathlike object or string representing a file

Movable volume. Maps to a command-line argument: --mov %s.

reg_outa string

Input/output registration file. Maps to a command-line argument: --reg %s.

target_filea pathlike object or string representing a file

Target volume. Maps to a command-line argument: --targ %s.

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: {})

noedita boolean

Do not open edit window (exit) - for conversions. Maps to a command-line argument: --noedit.

regheadera boolean

Compute registration from headers. Maps to a command-line argument: --regheader.

subject_ida string

Set subject id. Maps to a command-line argument: --s %s.

subjects_dira pathlike object or string representing an existing directory

Use dir as SUBJECTS_DIR. Maps to a command-line argument: --sd %s.

fslregout_filea pathlike object or string representing a file

Resulting FSL-Style registration matrix.

regout_filea pathlike object or string representing a file

Resulting registration file.

copyBrainMaskToFreesurfer

Link to code

Bases: nipype.interfaces.io.IOBase

Copy a custom brain mask in the freesurfer subject mri/ directory.

It replaces the brainmask files generated by Freesurfer recon-all

in order to re-run recon-all with a custom brain mask.

Examples

>>> from cmtklib.interfaces.freesurfer import copyBrainMaskToFreesurfer
>>> copy_mask_fs = copyBrainMaskToFreesurfer()
>>> copy_mask_fs.inputs.in_file = 'sub-01_desc-brain_mask.nii.gz'
>>> copy_mask_fs.inputs.subject_dir = '/path/to/output_dir/freesurfer/sub-01'
>>> copy_mask_fs.run()  

in_file : a pathlike object or string representing an existing file subject_dir : a pathlike object or string representing an existing directory

out_brainmask_file : a pathlike object or string representing an existing file out_brainmaskauto_file : a pathlike object or string representing an existing file

copyFileToFreesurfer

Link to code

Bases: nipype.interfaces.io.IOBase

Copy a file to an output specified.

Note

Not used.

in_file : a pathlike object or string representing an existing file out_file : a pathlike object or string representing a file

out_file : a pathlike object or string representing an existing file