nipype.interfaces.freesurfer.preprocess module¶
Provides interfaces to various commands provided by FreeSurfer
ApplyVolTransform¶
Bases: FSCommand
Wrapped executable:
mri_vol2vol
.Use FreeSurfer mri_vol2vol to apply a transform.
Examples
>>> from nipype.interfaces.freesurfer import ApplyVolTransform >>> applyreg = ApplyVolTransform() >>> applyreg.inputs.source_file = 'structural.nii' >>> applyreg.inputs.reg_file = 'register.dat' >>> applyreg.inputs.transformed_file = 'struct_warped.nii' >>> applyreg.inputs.fs_target = True >>> applyreg.cmdline 'mri_vol2vol --fstarg --reg register.dat --mov structural.nii --o struct_warped.nii'
- fs_targeta boolean
Use orig.mgz from subject in regfile as target. Maps to a command-line argument:
--fstarg
. Mutually exclusive with inputs:target_file
,tal
,fs_target
. Requires inputs:reg_file
.- fsl_reg_filea pathlike object or string representing an existing file
FslRAS-to-fslRAS matrix (FSL format). Maps to a command-line argument:
--fsl %s
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.- lta_filea pathlike object or string representing an existing file
Linear Transform Array file. Maps to a command-line argument:
--lta %s
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.- lta_inv_filea pathlike object or string representing an existing file
LTA, invert. Maps to a command-line argument:
--lta-inv %s
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.- mni_152_rega boolean
Target MNI152 space. Maps to a command-line argument:
--regheader
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.- reg_filea pathlike object or string representing an existing file
TkRAS-to-tkRAS matrix (tkregister2 format). Maps to a command-line argument:
--reg %s
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.- reg_headera boolean
ScannerRAS-to-ScannerRAS matrix = identity. Maps to a command-line argument:
--regheader
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.- source_filea pathlike object or string representing an existing file
Input volume you wish to transform. Maps to a command-line argument:
--mov %s
.- subjecta unicode string
Set matrix = identity and use subject for any templates. Maps to a command-line argument:
--s %s
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.- tala boolean
Map to a sub FOV of MNI305 (with –reg only). Maps to a command-line argument:
--tal
. Mutually exclusive with inputs:target_file
,tal
,fs_target
.- target_filea pathlike object or string representing an existing file
Output template volume. Maps to a command-line argument:
--targ %s
. Mutually exclusive with inputs:target_file
,tal
,fs_target
.- xfm_reg_filea pathlike object or string representing an existing file
ScannerRAS-to-ScannerRAS matrix (MNI format). Maps to a command-line argument:
--xfm %s
. Mutually exclusive with inputs:reg_file
,lta_file
,lta_inv_file
,fsl_reg_file
,xfm_reg_file
,reg_header
,mni_152_reg
,subject
.
- argsa unicode 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:
{}
)- interp‘trilin’ or ‘nearest’ or ‘cubic’
Interpolation method (<trilin> or nearest). Maps to a command-line argument:
--interp %s
.- inversea boolean
Sample from target to source. Maps to a command-line argument:
--inv
.- invert_morpha boolean
Compute and use the inverse of the non-linear morph to resample the input volume. To be used by –m3z. Maps to a command-line argument:
--inv-morph
. Requires inputs:m3z_file
.- m3z_filea pathlike object or string representing a file
This is the morph to be applied to the volume. Unless the morph is in mri/transforms (eg.: for talairach.m3z computed by reconall), you will need to specify the full path to this morph and use the –noDefM3zPath flag. Maps to a command-line argument:
--m3z %s
.- no_ded_m3z_patha boolean
To be used with the m3z flag. Instructs the code not to look for them3z morph in the default location (SUBJECTS_DIR/subj/mri/transforms), but instead just use the path indicated in –m3z. Maps to a command-line argument:
--noDefM3zPath
. Requires inputs:m3z_file
.- no_resamplea boolean
Do not resample; just change vox2ras matrix. Maps to a command-line argument:
--no-resample
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- tal_resolutiona float
Resolution to sample when using tal. Maps to a command-line argument:
--talres %.10f
.- transformed_filea pathlike object or string representing a file
Output volume. Maps to a command-line argument:
--o %s
.
- transformed_filea pathlike object or string representing an existing file
Path to output file if used normally.
BBRegister¶
Bases: 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. It is required that you have an anatomical scan of the subject that has already been recon-all-ed using freesurfer.
Examples
>>> from nipype.interfaces.freesurfer import BBRegister >>> bbreg = BBRegister(subject_id='me', source_file='structural.nii', init='header', contrast_type='t2') >>> bbreg.cmdline 'bbregister --t2 --init-header --reg structural_bbreg_me.dat --mov structural.nii --s me'
- contrast_type‘t1’ or ‘t2’ or ‘bold’ or ‘dti’
Contrast type of image. Maps to a command-line argument:
--%s
.- source_filea pathlike object or string representing a file
Source file to be registered. Maps to a command-line argument:
--mov %s
.- subject_ida unicode string
Freesurfer subject id. Maps to a command-line argument:
--s %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- dof6 or 9 or 12
Number of transform degrees of freedom. Maps to a command-line argument:
--%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:
{}
)- epi_maska boolean
Mask out B0 regions in stages 1 and 2. Maps to a command-line argument:
--epi-mask
.- fsldofan integer (int or long)
Degrees of freedom for initial registration (FSL). Maps to a command-line argument:
--fsl-dof %d
.- init‘coreg’ or ‘rr’ or ‘spm’ or ‘fsl’ or ‘header’ or ‘best’
Initialize registration with mri_coreg, spm, fsl, or header. Maps to a command-line argument:
--init-%s
. Mutually exclusive with inputs:init_reg_file
.- init_cost_filea boolean or a pathlike object or string representing a file
Output initial registration cost file. Maps to a command-line argument:
--initcost %s
.- init_reg_filea pathlike object or string representing an existing file
Existing registration file. Maps to a command-line argument:
--init-reg %s
. Mutually exclusive with inputs:init
.- 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_lta_filea boolean or a pathlike object or string representing a file
Write the transformation matrix in LTA format. Maps to a command-line argument:
--lta %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 (int or long)
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.
- init_cost_filea pathlike object or string representing an existing file
Output initial registration cost file.
- min_cost_filea pathlike object or string representing an existing file
Output registration minimum cost file.
- out_fsl_filea pathlike object or string representing an existing file
Output FLIRT-style registration file.
- out_lta_filea pathlike object or string representing an existing file
Output LTA-style registration file.
- out_reg_filea pathlike object or string representing an existing file
Output registration file.
- registered_filea pathlike object or string representing an existing file
Registered and resampled source file.
CALabel¶
Bases: FSCommandOpenMP
Wrapped executable:
mri_ca_label
.Label subcortical structures based in GCA model.
See also
For complete details, see the FS Documentation
Examples
>>> from nipype.interfaces import freesurfer >>> ca_label = freesurfer.CALabel() >>> ca_label.inputs.in_file = "norm.mgz" >>> ca_label.inputs.out_file = "out.mgz" >>> ca_label.inputs.transform = "trans.mat" >>> ca_label.inputs.template = "Template_6.nii" # in practice use .gcs extension >>> ca_label.cmdline 'mri_ca_label norm.mgz trans.mat Template_6.nii out.mgz'
- in_filea pathlike object or string representing an existing file
Input volume for CALabel. Maps to a command-line argument:
%s
(position: -4).- out_filea pathlike object or string representing a file
Output file for CALabel. Maps to a command-line argument:
%s
(position: -1).- templatea pathlike object or string representing an existing file
Input template for CALabel. Maps to a command-line argument:
%s
(position: -2).- transforma pathlike object or string representing an existing file
Input transform for CALabel. Maps to a command-line argument:
%s
(position: -3).
- aligna boolean
Align CALabel. Maps to a command-line argument:
-align
.- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- asega pathlike object or string representing an existing file
Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file. Maps to a command-line argument:
-aseg %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_vola pathlike object or string representing an existing file
Set input volume. Maps to a command-line argument:
-r %s
.- intensitiesa pathlike object or string representing an existing file
Input label intensities file(used in longitudinal processing). Maps to a command-line argument:
-r %s
.- labela pathlike object or string representing an existing file
Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file. Maps to a command-line argument:
-l %s
.- no_big_ventriclesa boolean
No big ventricles. Maps to a command-line argument:
-nobigventricles
.- num_threadsan integer (int or long)
Allows for specifying more threads.
- priora float
Prior for CALabel. Maps to a command-line argument:
-prior %.1f
.- relabel_unlikelya tuple of the form: (an integer (int or long), a float)
Reclassify voxels at least some std devs from the mean using some size Gaussian window. Maps to a command-line argument:
-relabel_unlikely %d %.1f
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- out_filea pathlike object or string representing a file
Output volume from CALabel.
CANormalize¶
Bases: FSCommand
Wrapped executable:
mri_ca_normalize
.This program creates a normalized volume using the brain volume and an input gca file.
See also
For complete details, see the FS Documentation.
Examples
>>> from nipype.interfaces import freesurfer >>> ca_normalize = freesurfer.CANormalize() >>> ca_normalize.inputs.in_file = "T1.mgz" >>> ca_normalize.inputs.atlas = "atlas.nii.gz" # in practice use .gca atlases >>> ca_normalize.inputs.transform = "trans.mat" # in practice use .lta transforms >>> ca_normalize.cmdline 'mri_ca_normalize T1.mgz atlas.nii.gz trans.mat T1_norm.mgz'
- atlasa pathlike object or string representing an existing file
The atlas file in gca format. Maps to a command-line argument:
%s
(position: -3).- in_filea pathlike object or string representing an existing file
The input file for CANormalize. Maps to a command-line argument:
%s
(position: -4).- transforma pathlike object or string representing an existing file
The tranform file in lta format. Maps to a command-line argument:
%s
(position: -2).
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- control_pointsa pathlike object or string representing a file
File name for the output control points. Maps to a command-line argument:
-c %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:
{}
)- long_filea pathlike object or string representing a file
Undocumented flag used in longitudinal processing. Maps to a command-line argument:
-long %s
.- maska pathlike object or string representing an existing file
Specifies volume to use as mask. Maps to a command-line argument:
-mask %s
.- out_filea pathlike object or string representing a file
The output file for CANormalize. Maps to a command-line argument:
%s
(position: -1).- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- control_pointsa pathlike object or string representing a file
The output control points for Normalize.
- out_filea pathlike object or string representing a file
The output file for Normalize.
CARegister¶
Bases: FSCommandOpenMP
Wrapped executable:
mri_ca_register
.Generates a multi-dimensional talairach transform from a gca file and talairach.lta file
See also
For complete details, see the FS Documentation
Examples
>>> from nipype.interfaces import freesurfer >>> ca_register = freesurfer.CARegister() >>> ca_register.inputs.in_file = "norm.mgz" >>> ca_register.inputs.out_file = "talairach.m3z" >>> ca_register.cmdline 'mri_ca_register norm.mgz talairach.m3z'
- in_filea pathlike object or string representing an existing file
The input volume for CARegister. Maps to a command-line argument:
%s
(position: -3).
- Aan integer (int or long)
Undocumented flag used in longitudinal processing. Maps to a command-line argument:
-A %d
.- aligna string
Specifies when to perform alignment. Maps to a command-line argument:
-align-%s
.- argsa unicode 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:
{}
)- invert_and_savea boolean
Invert and save the .m3z multi-dimensional talaraich transform to x, y, and z .mgz files. Maps to a command-line argument:
-invert-and-save
(position: -4).- l_filesa list of items which are a pathlike object or string representing a file
Undocumented flag used in longitudinal processing. Maps to a command-line argument:
-l %s
.- levelsan integer (int or long)
Defines how many surrounding voxels will be used in interpolations, default is 6. Maps to a command-line argument:
-levels %d
.- maska pathlike object or string representing an existing file
Specifies volume to use as mask. Maps to a command-line argument:
-mask %s
.- no_big_ventriclesa boolean
No big ventricles. Maps to a command-line argument:
-nobigventricles
.- num_threadsan integer (int or long)
Allows for specifying more threads.
- out_filea pathlike object or string representing a file
The output volume for CARegister. Maps to a command-line argument:
%s
(position: -1).- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- templatea pathlike object or string representing an existing file
The template file in gca format. Maps to a command-line argument:
%s
(position: -2).- transforma pathlike object or string representing an existing file
Specifies transform in lta format. Maps to a command-line argument:
-T %s
.
- out_filea pathlike object or string representing a file
The output file for CARegister.
ConcatenateLTA¶
Bases: FSCommand
Wrapped executable:
mri_concatenate_lta
.Concatenates two consecutive LTA transformations into one overall transformation
Out = LTA2*LTA1
Examples
>>> from nipype.interfaces.freesurfer import ConcatenateLTA >>> conc_lta = ConcatenateLTA() >>> conc_lta.inputs.in_lta1 = 'lta1.lta' >>> conc_lta.inputs.in_lta2 = 'lta2.lta' >>> conc_lta.cmdline 'mri_concatenate_lta lta1.lta lta2.lta lta1_concat.lta'You can use ‘identity.nofile’ as the filename for in_lta2, e.g.:
>>> conc_lta.inputs.in_lta2 = 'identity.nofile' >>> conc_lta.inputs.invert_1 = True >>> conc_lta.inputs.out_file = 'inv1.lta' >>> conc_lta.cmdline 'mri_concatenate_lta -invert1 lta1.lta identity.nofile inv1.lta'To create a RAS2RAS transform:
>>> conc_lta.inputs.out_type = 'RAS2RAS' >>> conc_lta.cmdline 'mri_concatenate_lta -invert1 -out_type 1 lta1.lta identity.nofile inv1.lta'
- in_lta1a pathlike object or string representing an existing file
Maps some src1 to dst1. Maps to a command-line argument:
%s
(position: -3).- in_lta2a pathlike object or string representing an existing file or ‘identity.nofile’
Maps dst1(src2) to dst2. Maps to a command-line argument:
%s
(position: -2).
- argsa unicode 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:
{}
)- invert_1a boolean
Invert in_lta1 before applying it. Maps to a command-line argument:
-invert1
.- invert_2a boolean
Invert in_lta2 before applying it. Maps to a command-line argument:
-invert2
.- invert_outa boolean
Invert output LTA. Maps to a command-line argument:
-invertout
.- out_filea pathlike object or string representing a file
The combined LTA maps: src1 to dst2 = LTA2*LTA1. Maps to a command-line argument:
%s
(position: -1).- out_type‘VOX2VOX’ or ‘RAS2RAS’
Set final LTA type. Maps to a command-line argument:
-out_type %d
.- subjecta unicode string
Set subject in output LTA. Maps to a command-line argument:
-subject %s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- tal_source_filea pathlike object or string representing an existing file
If in_lta2 is talairach.xfm, specify source for talairach. Maps to a command-line argument:
-tal %s
(position: -5). Requires inputs:tal_template_file
.- tal_template_filea pathlike object or string representing an existing file
If in_lta2 is talairach.xfm, specify template for talairach. Maps to a command-line argument:
%s
(position: -4). Requires inputs:tal_source_file
.
- out_filea pathlike object or string representing a file
The combined LTA maps: src1 to dst2 = LTA2*LTA1.
DICOMConvert¶
Bases: FSCommand
Wrapped executable:
mri_convert
.use fs mri_convert to convert dicom files
Examples
>>> from nipype.interfaces.freesurfer import DICOMConvert >>> cvt = DICOMConvert() >>> cvt.inputs.dicom_dir = 'dicomdir' >>> cvt.inputs.file_mapping = [('nifti', '*.nii'), ('info', 'dicom*.txt'), ('dti', '*dti.bv*')]
- base_output_dira pathlike object or string representing a directory
Directory in which subject directories are created.
- dicom_dira pathlike object or string representing an existing directory
Dicom directory from which to convert dicom files.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- dicom_infoa pathlike object or string representing an existing file
File containing summary information from mri_parse_sdcmdir.
- 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:
{}
)- file_mappinga list of items which are a tuple of the form: (a unicode string, a unicode string)
Defines the output fields of interface.
- ignore_single_slicea boolean
Ignore volumes containing a single slice. Requires inputs:
dicom_info
.- out_type‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’
Defines the type of output file produced. (Nipype default value:
niigz
)- seq_lista list of items which are a unicode string
List of pulse sequence names to be converted. Requires inputs:
dicom_info
.- subject_dir_templatea unicode string
Template for subject directory name. (Nipype default value:
S.%04d
)- subject_idany value
Subject identifier to insert into template.
- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- property DICOMConvert.cmdline¶
command plus any arguments (args) validates arguments and generates command line
EditWMwithAseg¶
Bases: FSCommand
Wrapped executable:
mri_edit_wm_with_aseg
.Edits a wm file using a segmentation
Examples
>>> from nipype.interfaces.freesurfer import EditWMwithAseg >>> editwm = EditWMwithAseg() >>> editwm.inputs.in_file = "T1.mgz" >>> editwm.inputs.brain_file = "norm.mgz" >>> editwm.inputs.seg_file = "aseg.mgz" >>> editwm.inputs.out_file = "wm.asegedit.mgz" >>> editwm.inputs.keep_in = True >>> editwm.cmdline 'mri_edit_wm_with_aseg -keep-in T1.mgz norm.mgz aseg.mgz wm.asegedit.mgz'
- brain_filea pathlike object or string representing an existing file
Input brain/T1 file. Maps to a command-line argument:
%s
(position: -3).- in_filea pathlike object or string representing an existing file
Input white matter segmentation file. Maps to a command-line argument:
%s
(position: -4).- out_filea pathlike object or string representing a file
File to be written as output. Maps to a command-line argument:
%s
(position: -1).- seg_filea pathlike object or string representing an existing file
Input presurf segmentation file. Maps to a command-line argument:
%s
(position: -2).
- argsa unicode 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:
{}
)- keep_ina boolean
Keep edits as found in input volume. Maps to a command-line argument:
-keep-in
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- out_filea pathlike object or string representing a file
Output edited WM file.
FitMSParams¶
Bases: FSCommand
Wrapped executable:
mri_ms_fitparms
.Estimate tissue paramaters from a set of FLASH images.
Examples
>>> from nipype.interfaces.freesurfer import FitMSParams >>> msfit = FitMSParams() >>> msfit.inputs.in_files = ['flash_05.mgz', 'flash_30.mgz'] >>> msfit.inputs.out_dir = 'flash_parameters' >>> msfit.cmdline 'mri_ms_fitparms flash_05.mgz flash_30.mgz flash_parameters'
- in_filesa list of items which are a pathlike object or string representing an existing file
List of FLASH images (must be in mgh format). Maps to a command-line argument:
%s
(position: -2).
- argsa unicode 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:
{}
)- flip_lista list of items which are an integer (int or long)
List of flip angles of the input files.
- out_dira pathlike object or string representing a directory
Directory to store output in. Maps to a command-line argument:
%s
(position: -1).- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- te_lista list of items which are a float
List of TEs of the input files (in msec).
- tr_lista list of items which are an integer (int or long)
List of TRs of the input files (in msec).
- xfm_lista list of items which are a pathlike object or string representing an existing file
List of transform files to apply to each FLASH image.
- pd_imagea pathlike object or string representing an existing file
Image of estimated proton density values.
- t1_imagea pathlike object or string representing an existing file
Image of estimated T1 relaxation values.
- t2star_imagea pathlike object or string representing an existing file
Image of estimated T2* values.
MNIBiasCorrection¶
Bases: FSCommand
Wrapped executable:
mri_nu_correct.mni
.Wrapper for nu_correct, a program from the Montreal Neurological Insitute (MNI) used for correcting intensity non-uniformity (ie, bias fields). You must have the MNI software installed on your system to run this. See [www.bic.mni.mcgill.ca/software/N3] for more info.
mri_nu_correct.mni uses float internally instead of uchar. It also rescales the output so that the global mean is the same as that of the input. These two changes are linked and can be turned off with –no-float
Examples
>>> from nipype.interfaces.freesurfer import MNIBiasCorrection >>> correct = MNIBiasCorrection() >>> correct.inputs.in_file = "norm.mgz" >>> correct.inputs.iterations = 6 >>> correct.inputs.protocol_iterations = 1000 >>> correct.inputs.distance = 50 >>> correct.cmdline 'mri_nu_correct.mni --distance 50 --i norm.mgz --n 6 --o norm_output.mgz --proto-iters 1000'References
[http://freesurfer.net/fswiki/mri_nu_correct.mni] [http://www.bic.mni.mcgill.ca/software/N3] [https://github.com/BIC-MNI/N3]
- in_filea pathlike object or string representing an existing file
Input volume. Input can be any format accepted by mri_convert. Maps to a command-line argument:
--i %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- distancean integer (int or long)
N3 -distance option. Maps to a command-line argument:
--distance %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:
{}
)- iterationsan integer (int or long)
Number of iterations to run nu_correct. Default is 4. This is the number of times that nu_correct is repeated (ie, using the output from the previous run as the input for the next). This is different than the -iterations option to nu_correct. Maps to a command-line argument:
--n %d
. (Nipype default value:4
)- maska pathlike object or string representing an existing file
Brainmask volume. Input can be any format accepted by mri_convert. Maps to a command-line argument:
--mask %s
.- no_rescalea boolean
Do not rescale so that global mean of output == input global mean. Maps to a command-line argument:
--no-rescale
.- out_filea pathlike object or string representing a file
Output volume. Output can be any format accepted by mri_convert. If the output format is COR, then the directory must exist. Maps to a command-line argument:
--o %s
.- protocol_iterationsan integer (int or long)
Passes Np as argument of the -iterations flag of nu_correct. This is different than the –n flag above. Default is not to pass nu_correct the -iterations flag. Maps to a command-line argument:
--proto-iters %d
.- shrinkan integer (int or long)
Shrink parameter for finer sampling (default is 4). Maps to a command-line argument:
--shrink %d
.- stopa float
Convergence threshold below which iteration stops (suggest 0.01 to 0.0001). Maps to a command-line argument:
--stop %f
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- transforma pathlike object or string representing an existing file
Tal.xfm. Use mri_make_uchar instead of conforming. Maps to a command-line argument:
--uchar %s
.
- out_filea pathlike object or string representing an existing file
Output volume.
MRIConvert¶
Bases: FSCommand
Wrapped executable:
mri_convert
.use fs mri_convert to manipulate files
Note
Adds niigz as an output type option
Examples
>>> mc = MRIConvert() >>> mc.inputs.in_file = 'structural.nii' >>> mc.inputs.out_file = 'outfile.mgz' >>> mc.inputs.out_type = 'mgz' >>> mc.cmdline 'mri_convert --out_type mgz --input_volume structural.nii --output_volume outfile.mgz'
- in_filea pathlike object or string representing an existing file
File to read/convert. Maps to a command-line argument:
--input_volume %s
(position: -2).
- apply_inv_transforma pathlike object or string representing an existing file
Apply inverse transformation xfm file. Maps to a command-line argument:
--apply_inverse_transform %s
.- apply_transforma pathlike object or string representing an existing file
Apply xfm file. Maps to a command-line argument:
--apply_transform %s
.- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- asciia boolean
Save output as ascii col>row>slice>frame. Maps to a command-line argument:
--ascii
.- autoalign_matrixa pathlike object or string representing an existing file
Text file with autoalign matrix. Maps to a command-line argument:
--autoalign %s
.- color_filea pathlike object or string representing an existing file
Color file. Maps to a command-line argument:
--color_file %s
.- conforma boolean
Conform to 1mm voxel size in coronal slice direction with 256^3 or more. Maps to a command-line argument:
--conform
.- conform_mina boolean
Conform to smallest size. Maps to a command-line argument:
--conform_min
.- conform_sizea float
Conform to size_in_mm. Maps to a command-line argument:
--conform_size %s
.- crop_centera tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
<x> <y> <z> crop to 256 around center (x, y, z). Maps to a command-line argument:
--crop %d %d %d
.- crop_gdfa boolean
Apply GDF cropping. Maps to a command-line argument:
--crop_gdf
.- crop_sizea tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
<dx> <dy> <dz> crop to size <dx, dy, dz>. Maps to a command-line argument:
--cropsize %d %d %d
.- cut_endsan integer (int or long)
Remove ncut slices from the ends. Maps to a command-line argument:
--cutends %d
.- cw256a boolean
Confrom to dimensions of 256^3. Maps to a command-line argument:
--cw256
.- devolve_transforma unicode string
Subject id. Maps to a command-line argument:
--devolvexfm %s
.- drop_nan integer (int or long)
Drop the last n frames. Maps to a command-line argument:
--ndrop %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:
{}
)- fill_parcellationa boolean
Fill parcellation. Maps to a command-line argument:
--fill_parcellation
.- force_rasa boolean
Use default when orientation info absent. Maps to a command-line argument:
--force_ras_good
.- framean integer (int or long)
Keep only 0-based frame number. Maps to a command-line argument:
--frame %d
.- frame_subsamplea tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
Start delta end : frame subsampling (end = -1 for end). Maps to a command-line argument:
--fsubsample %d %d %d
.- fwhma float
Smooth input volume by fwhm mm. Maps to a command-line argument:
--fwhm %f
.- in_centera list of at most 3 items which are a float
<R coordinate> <A coordinate> <S coordinate>. Maps to a command-line argument:
--in_center %s
.- in_i_dira tuple of the form: (a float, a float, a float)
<R direction> <A direction> <S direction>. Maps to a command-line argument:
--in_i_direction %f %f %f
.- in_i_sizean integer (int or long)
Input i size. Maps to a command-line argument:
--in_i_size %d
.- in_infoa boolean
Display input info. Maps to a command-line argument:
--in_info
.- in_j_dira tuple of the form: (a float, a float, a float)
<R direction> <A direction> <S direction>. Maps to a command-line argument:
--in_j_direction %f %f %f
.- in_j_sizean integer (int or long)
Input j size. Maps to a command-line argument:
--in_j_size %d
.- in_k_dira tuple of the form: (a float, a float, a float)
<R direction> <A direction> <S direction>. Maps to a command-line argument:
--in_k_direction %f %f %f
.- in_k_sizean integer (int or long)
Input k size. Maps to a command-line argument:
--in_k_size %d
.- in_likea pathlike object or string representing an existing file
Input looks like. Maps to a command-line argument:
--in_like %s
.- in_matrixa boolean
Display input matrix. Maps to a command-line argument:
--in_matrix
.- in_orientation‘LAI’ or ‘LIA’ or ‘ALI’ or ‘AIL’ or ‘ILA’ or ‘IAL’ or ‘LAS’ or ‘LSA’ or ‘ALS’ or ‘ASL’ or ‘SLA’ or ‘SAL’ or ‘LPI’ or ‘LIP’ or ‘PLI’ or ‘PIL’ or ‘ILP’ or ‘IPL’ or ‘LPS’ or ‘LSP’ or ‘PLS’ or ‘PSL’ or ‘SLP’ or ‘SPL’ or ‘RAI’ or ‘RIA’ or ‘ARI’ or ‘AIR’ or ‘IRA’ or ‘IAR’ or ‘RAS’ or ‘RSA’ or ‘ARS’ or ‘ASR’ or ‘SRA’ or ‘SAR’ or ‘RPI’ or ‘RIP’ or ‘PRI’ or ‘PIR’ or ‘IRP’ or ‘IPR’ or ‘RPS’ or ‘RSP’ or ‘PRS’ or ‘PSR’ or ‘SRP’ or ‘SPR’
Specify the input orientation. Maps to a command-line argument:
--in_orientation %s
.- in_scalea float
Input intensity scale factor. Maps to a command-line argument:
--scale %f
.- in_statsa boolean
Display input stats. Maps to a command-line argument:
--in_stats
.- in_type‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’ or ‘ge’ or ‘gelx’ or ‘lx’ or ‘ximg’ or ‘siemens’ or ‘dicom’ or ‘siemens_dicom’
Input file type. Maps to a command-line argument:
--in_type %s
.- invert_contrasta float
Threshold for inversting contrast. Maps to a command-line argument:
--invert_contrast %f
.- midframea boolean
Keep only the middle frame. Maps to a command-line argument:
--mid-frame
.- no_changea boolean
Don’t change type of input to that of template. Maps to a command-line argument:
--nochange
.- no_scalea boolean
Dont rescale values for COR. Maps to a command-line argument:
--no_scale 1
.- no_translatea boolean
???. Maps to a command-line argument:
--no_translate
.- no_writea boolean
Do not write output. Maps to a command-line argument:
--no_write
.- out_centera tuple of the form: (a float, a float, a float)
<R coordinate> <A coordinate> <S coordinate>. Maps to a command-line argument:
--out_center %f %f %f
.- out_datatype‘uchar’ or ‘short’ or ‘int’ or ‘float’
Output data type <uchar|short|int|float>. Maps to a command-line argument:
--out_data_type %s
.- out_filea pathlike object or string representing a file
Output filename or True to generate one. Maps to a command-line argument:
--output_volume %s
(position: -1).- out_i_countan integer (int or long)
Some count ?? in i direction. Maps to a command-line argument:
--out_i_count %d
.- out_i_dira tuple of the form: (a float, a float, a float)
<R direction> <A direction> <S direction>. Maps to a command-line argument:
--out_i_direction %f %f %f
.- out_i_sizean integer (int or long)
Output i size. Maps to a command-line argument:
--out_i_size %d
.- out_infoa boolean
Display output info. Maps to a command-line argument:
--out_info
.- out_j_countan integer (int or long)
Some count ?? in j direction. Maps to a command-line argument:
--out_j_count %d
.- out_j_dira tuple of the form: (a float, a float, a float)
<R direction> <A direction> <S direction>. Maps to a command-line argument:
--out_j_direction %f %f %f
.- out_j_sizean integer (int or long)
Output j size. Maps to a command-line argument:
--out_j_size %d
.- out_k_countan integer (int or long)
Some count ?? in k direction. Maps to a command-line argument:
--out_k_count %d
.- out_k_dira tuple of the form: (a float, a float, a float)
<R direction> <A direction> <S direction>. Maps to a command-line argument:
--out_k_direction %f %f %f
.- out_k_sizean integer (int or long)
Output k size. Maps to a command-line argument:
--out_k_size %d
.- out_matrixa boolean
Display output matrix. Maps to a command-line argument:
--out_matrix
.- out_orientation‘LAI’ or ‘LIA’ or ‘ALI’ or ‘AIL’ or ‘ILA’ or ‘IAL’ or ‘LAS’ or ‘LSA’ or ‘ALS’ or ‘ASL’ or ‘SLA’ or ‘SAL’ or ‘LPI’ or ‘LIP’ or ‘PLI’ or ‘PIL’ or ‘ILP’ or ‘IPL’ or ‘LPS’ or ‘LSP’ or ‘PLS’ or ‘PSL’ or ‘SLP’ or ‘SPL’ or ‘RAI’ or ‘RIA’ or ‘ARI’ or ‘AIR’ or ‘IRA’ or ‘IAR’ or ‘RAS’ or ‘RSA’ or ‘ARS’ or ‘ASR’ or ‘SRA’ or ‘SAR’ or ‘RPI’ or ‘RIP’ or ‘PRI’ or ‘PIR’ or ‘IRP’ or ‘IPR’ or ‘RPS’ or ‘RSP’ or ‘PRS’ or ‘PSR’ or ‘SRP’ or ‘SPR’
Specify the output orientation. Maps to a command-line argument:
--out_orientation %s
.- out_scalea float
Output intensity scale factor. Maps to a command-line argument:
--out-scale %d
.- out_statsa boolean
Display output stats. Maps to a command-line argument:
--out_stats
.- out_type‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’
Output file type. Maps to a command-line argument:
--out_type %s
.- parse_onlya boolean
Parse input only. Maps to a command-line argument:
--parse_only
.- read_onlya boolean
Read the input volume. Maps to a command-line argument:
--read_only
.- reordera tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))
Olddim1 olddim2 olddim3. Maps to a command-line argument:
--reorder %d %d %d
.- resample_type‘interpolate’ or ‘weighted’ or ‘nearest’ or ‘sinc’ or ‘cubic’
<interpolate|weighted|nearest|sinc|cubic> (default is interpolate). Maps to a command-line argument:
--resample_type %s
.- reslice_likea pathlike object or string representing an existing file
Reslice output to match file. Maps to a command-line argument:
--reslice_like %s
.- sdcm_lista pathlike object or string representing an existing file
List of DICOM files for conversion. Maps to a command-line argument:
--sdcmlist %s
.- skip_nan integer (int or long)
Skip the first n frames. Maps to a command-line argument:
--nskip %d
.- slice_biasa float
Apply half-cosine bias field. Maps to a command-line argument:
--slice-bias %f
.- slice_cropa tuple of the form: (an integer (int or long), an integer (int or long))
S_start s_end : keep slices s_start to s_end. Maps to a command-line argument:
--slice-crop %d %d
.- slice_reversea boolean
Reverse order of slices, update vox2ras. Maps to a command-line argument:
--slice-reverse
.- smooth_parcellationa boolean
Smooth parcellation. Maps to a command-line argument:
--smooth_parcellation
.- sphinxa boolean
Change orientation info to sphinx. Maps to a command-line argument:
--sphinx
.- splita boolean
Split output frames into separate output files. Maps to a command-line argument:
--split
.- status_filea pathlike object or string representing a file
Status file for DICOM conversion. Maps to a command-line argument:
--status %s
.- subject_namea unicode string
Subject name ???. Maps to a command-line argument:
--subject_name %s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- tean integer (int or long)
TE in msec. Maps to a command-line argument:
-te %d
.- template_infoa boolean
Dump info about template. Maps to a command-line argument:
--template_info
.- template_type‘cor’ or ‘mgh’ or ‘mgz’ or ‘minc’ or ‘analyze’ or ‘analyze4d’ or ‘spm’ or ‘afni’ or ‘brik’ or ‘bshort’ or ‘bfloat’ or ‘sdt’ or ‘outline’ or ‘otl’ or ‘gdf’ or ‘nifti1’ or ‘nii’ or ‘niigz’ or ‘ge’ or ‘gelx’ or ‘lx’ or ‘ximg’ or ‘siemens’ or ‘dicom’ or ‘siemens_dicom’
Template file type. Maps to a command-line argument:
--template_type %s
.- tian integer (int or long)
TI in msec (note upper case flag). Maps to a command-line argument:
-ti %d
.- tran integer (int or long)
TR in msec. Maps to a command-line argument:
-tr %d
.- unwarp_gradienta boolean
Unwarp gradient nonlinearity. Maps to a command-line argument:
--unwarp_gradient_nonlinearity
.- vox_sizea tuple of the form: (a float, a float, a float)
<size_x> <size_y> <size_z> specify the size (mm) - useful for upsampling or downsampling. Maps to a command-line argument:
-voxsize %f %f %f
.- zero_ge_z_offseta boolean
Zero ge z offset ???. Maps to a command-line argument:
--zero_ge_z_offset
.- zero_outlinesa boolean
Zero outlines. Maps to a command-line argument:
--zero_outlines
.
- out_filea list of items which are a pathlike object or string representing an existing file
Converted output file.
- MRIConvert.filemap = {'afni': 'brik', 'analyze': 'img', 'analyze4d': 'img', 'bfloat': 'bfloat', 'brik': 'brik', 'bshort': 'bshort', 'cor': 'cor', 'mgh': 'mgh', 'mgz': 'mgz', 'minc': 'mnc', 'nifti1': 'img', 'nii': 'nii', 'niigz': 'nii.gz', 'spm': 'img'}¶
MRIsCALabel¶
Bases: FSCommandOpenMP
Wrapped executable:
mris_ca_label
.For a single subject, produces an annotation file, in which each cortical surface vertex is assigned a neuroanatomical label.This automatic procedure employs data from a previously-prepared atlas file. An atlas file is created from a training set, capturing region data manually drawn by neuroanatomists combined with statistics on variability correlated to geometric information derived from the cortical model (sulcus and curvature). Besides the atlases provided with FreeSurfer, new ones can be prepared using mris_ca_train).
Examples
>>> from nipype.interfaces import freesurfer >>> ca_label = freesurfer.MRIsCALabel() >>> ca_label.inputs.subject_id = "test" >>> ca_label.inputs.hemisphere = "lh" >>> ca_label.inputs.canonsurf = "lh.pial" >>> ca_label.inputs.curv = "lh.pial" >>> ca_label.inputs.sulc = "lh.pial" >>> ca_label.inputs.classifier = "im1.nii" # in pracice, use .gcs extension >>> ca_label.inputs.smoothwm = "lh.pial" >>> ca_label.cmdline 'mris_ca_label test lh lh.pial im1.nii lh.aparc.annot'
- canonsurfa pathlike object or string representing an existing file
Input canonical surface file. Maps to a command-line argument:
%s
(position: -3).- classifiera pathlike object or string representing an existing file
Classifier array input file. Maps to a command-line argument:
%s
(position: -2).- curva pathlike object or string representing an existing file
Implicit input {hemisphere}.curv.
- hemisphere‘lh’ or ‘rh’
Hemisphere (‘lh’ or ‘rh’). Maps to a command-line argument:
%s
(position: -4).- smoothwma pathlike object or string representing an existing file
Implicit input {hemisphere}.smoothwm.
- subject_ida string
Subject name or ID. Maps to a command-line argument:
%s
(position: -5). (Nipype default value:subject_id
)- sulca pathlike object or string representing an existing file
Implicit input {hemisphere}.sulc.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- asega pathlike object or string representing an existing file
Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file. Maps to a command-line argument:
-aseg %s
.- copy_inputsa boolean
Copies implicit inputs to node directory and creates a temp subjects_directory. Use this when running as a node.
- 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:
{}
)- labela pathlike object or string representing an existing file
Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file. Maps to a command-line argument:
-l %s
.- num_threadsan integer (int or long)
Allows for specifying more threads.
- out_filea pathlike object or string representing a file
Annotated surface output file. Maps to a command-line argument:
%s
(position: -1).- seedan integer (int or long)
Maps to a command-line argument:
-seed %d
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- out_filea pathlike object or string representing a file
Output volume from MRIsCALabel.
- MRIsCALabel.run(**inputs)¶
Execute this interface.
This interface will not raise an exception if runtime.returncode is non-zero.
- Parameters
cwd (specify a folder where the interface should be run) –
inputs (allows the interface settings to be updated) –
- Returns
results – A copy of the instance that was executed, provenance information and, if successful, results
- Return type
Normalize¶
Bases: FSCommand
Wrapped executable:
mri_normalize
.Normalize the white-matter, optionally based on control points. The input volume is converted into a new volume where white matter image values all range around 110.
Examples
>>> from nipype.interfaces import freesurfer >>> normalize = freesurfer.Normalize() >>> normalize.inputs.in_file = "T1.mgz" >>> normalize.inputs.gradient = 1 >>> normalize.cmdline 'mri_normalize -g 1 T1.mgz T1_norm.mgz'
- in_filea pathlike object or string representing an existing file
The input file for Normalize. Maps to a command-line argument:
%s
(position: -2).
- argsa unicode 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:
{}
)- gradientan integer (int or long)
Use max intensity/mm gradient g (default=1). Maps to a command-line argument:
-g %d
.- maska pathlike object or string representing an existing file
The input mask file for Normalize. Maps to a command-line argument:
-mask %s
.- out_filea pathlike object or string representing a file
The output file for Normalize. Maps to a command-line argument:
%s
(position: -1).- segmentationa pathlike object or string representing an existing file
The input segmentation for Normalize. Maps to a command-line argument:
-aseg %s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- transforma pathlike object or string representing an existing file
Tranform file from the header of the input file.
- out_filea pathlike object or string representing a file
The output file for Normalize.
ParseDICOMDir¶
Bases: FSCommand
Wrapped executable:
mri_parse_sdcmdir
.Uses mri_parse_sdcmdir to get information from dicom directories
Examples
>>> from nipype.interfaces.freesurfer import ParseDICOMDir >>> dcminfo = ParseDICOMDir() >>> dcminfo.inputs.dicom_dir = '.' >>> dcminfo.inputs.sortbyrun = True >>> dcminfo.inputs.summarize = True >>> dcminfo.cmdline 'mri_parse_sdcmdir --d . --o dicominfo.txt --sortbyrun --summarize'
- dicom_dira pathlike object or string representing an existing directory
Path to siemens dicom directory. Maps to a command-line argument:
--d %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- dicom_info_filea pathlike object or string representing a file
File to which results are written. Maps to a command-line argument:
--o %s
. (Nipype default value:dicominfo.txt
)- 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:
{}
)- sortbyruna boolean
Assign run numbers. Maps to a command-line argument:
--sortbyrun
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- summarizea boolean
Only print out info for run leaders. Maps to a command-line argument:
--summarize
.
- dicom_info_filea pathlike object or string representing an existing file
Text file containing dicom information.
ReconAll¶
Bases: CommandLine
Wrapped executable:
recon-all
.Uses recon-all to generate surfaces and parcellations of structural data from anatomical images of a subject.
Examples
>>> from nipype.interfaces.freesurfer import ReconAll >>> reconall = ReconAll() >>> reconall.inputs.subject_id = 'foo' >>> reconall.inputs.directive = 'all' >>> reconall.inputs.subjects_dir = '.' >>> reconall.inputs.T1_files = 'structural.nii' >>> reconall.cmdline 'recon-all -all -i structural.nii -subjid foo -sd .' >>> reconall.inputs.flags = "-qcache" >>> reconall.cmdline 'recon-all -all -i structural.nii -qcache -subjid foo -sd .' >>> reconall.inputs.flags = ["-cw256", "-qcache"] >>> reconall.cmdline 'recon-all -all -i structural.nii -cw256 -qcache -subjid foo -sd .'Hemisphere may be specified regardless of directive:
>>> reconall.inputs.flags = [] >>> reconall.inputs.hemi = 'lh' >>> reconall.cmdline 'recon-all -all -i structural.nii -hemi lh -subjid foo -sd .'
-autorecon-hemi
uses the-hemi
input to specify the hemisphere to operate upon:>>> reconall.inputs.directive = 'autorecon-hemi' >>> reconall.cmdline 'recon-all -autorecon-hemi lh -i structural.nii -subjid foo -sd .'Hippocampal subfields can accept T1 and T2 images:
>>> reconall_subfields = ReconAll() >>> reconall_subfields.inputs.subject_id = 'foo' >>> reconall_subfields.inputs.directive = 'all' >>> reconall_subfields.inputs.subjects_dir = '.' >>> reconall_subfields.inputs.T1_files = 'structural.nii' >>> reconall_subfields.inputs.hippocampal_subfields_T1 = True >>> reconall_subfields.cmdline 'recon-all -all -i structural.nii -hippocampal-subfields-T1 -subjid foo -sd .' >>> reconall_subfields.inputs.hippocampal_subfields_T2 = ( ... 'structural.nii', 'test') >>> reconall_subfields.cmdline 'recon-all -all -i structural.nii -hippocampal-subfields-T1T2 structural.nii test -subjid foo -sd .' >>> reconall_subfields.inputs.hippocampal_subfields_T1 = False >>> reconall_subfields.cmdline 'recon-all -all -i structural.nii -hippocampal-subfields-T2 structural.nii test -subjid foo -sd .'
- FLAIR_filea pathlike object or string representing an existing file
Convert FLAIR image to orig directory. Maps to a command-line argument:
-FLAIR %s
.- T1_filesa list of items which are a pathlike object or string representing an existing file
Name of T1 file to process. Maps to a command-line argument:
-i %s...
.- T2_filea pathlike object or string representing an existing file
Convert T2 image to orig directory. Maps to a command-line argument:
-T2 %s
.- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- big_ventriclesa boolean
For use in subjects with enlarged ventricles. Maps to a command-line argument:
-bigventricles
.- brainstema boolean
Segment brainstem structures. Maps to a command-line argument:
-brainstem-structures
.- directive‘all’ or ‘autorecon1’ or ‘autorecon2’ or ‘autorecon2-volonly’ or ‘autorecon2-perhemi’ or ‘autorecon2-inflate1’ or ‘autorecon2-cp’ or ‘autorecon2-wm’ or ‘autorecon3’ or ‘autorecon3-T2pial’ or ‘autorecon-pial’ or ‘autorecon-hemi’ or ‘localGI’ or ‘qcache’
Process directive. Maps to a command-line argument:
-%s
(position: 0). (Nipype default value:all
)- 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:
{}
)- experta pathlike object or string representing an existing file
Set parameters using expert file. Maps to a command-line argument:
-expert %s
.- flagsa list of items which are a unicode string
Additional parameters. Maps to a command-line argument:
%s
.- hemi‘lh’ or ‘rh’
Hemisphere to process. Maps to a command-line argument:
-hemi %s
.- hippocampal_subfields_T1a boolean
Segment hippocampal subfields using input T1 scan. Maps to a command-line argument:
-hippocampal-subfields-T1
.- hippocampal_subfields_T2a tuple of the form: (a pathlike object or string representing an existing file, a unicode string)
Segment hippocampal subfields using T2 scan, identified by ID (may be combined with hippocampal_subfields_T1). Maps to a command-line argument:
-hippocampal-subfields-T2 %s %s
.- hiresa boolean
Conform to minimum voxel size (for voxels < 1mm). Maps to a command-line argument:
-hires
.- mpragea boolean
Assume scan parameters are MGH MP-RAGE protocol, which produces darker gray matter. Maps to a command-line argument:
-mprage
.- mri_aparc2asega unicode string
Flags to pass to mri_aparc2aseg commands. Mutually exclusive with inputs:
expert
.- mri_ca_labela unicode string
Flags to pass to mri_ca_label commands. Mutually exclusive with inputs:
expert
.- mri_ca_normalizea unicode string
Flags to pass to mri_ca_normalize commands. Mutually exclusive with inputs:
expert
.- mri_ca_registera unicode string
Flags to pass to mri_ca_register commands. Mutually exclusive with inputs:
expert
.- mri_edit_wm_with_asega unicode string
Flags to pass to mri_edit_wm_with_aseg commands. Mutually exclusive with inputs:
expert
.- mri_em_registera unicode string
Flags to pass to mri_em_register commands. Mutually exclusive with inputs:
expert
.- mri_filla unicode string
Flags to pass to mri_fill commands. Mutually exclusive with inputs:
expert
.- mri_maska unicode string
Flags to pass to mri_mask commands. Mutually exclusive with inputs:
expert
.- mri_normalizea unicode string
Flags to pass to mri_normalize commands. Mutually exclusive with inputs:
expert
.- mri_pretessa unicode string
Flags to pass to mri_pretess commands. Mutually exclusive with inputs:
expert
.- mri_remove_necka unicode string
Flags to pass to mri_remove_neck commands. Mutually exclusive with inputs:
expert
.- mri_segmenta unicode string
Flags to pass to mri_segment commands. Mutually exclusive with inputs:
expert
.- mri_segstatsa unicode string
Flags to pass to mri_segstats commands. Mutually exclusive with inputs:
expert
.- mri_tessellatea unicode string
Flags to pass to mri_tessellate commands. Mutually exclusive with inputs:
expert
.- mri_watersheda unicode string
Flags to pass to mri_watershed commands. Mutually exclusive with inputs:
expert
.- mris_anatomical_statsa unicode string
Flags to pass to mris_anatomical_stats commands. Mutually exclusive with inputs:
expert
.- mris_ca_labela unicode string
Flags to pass to mris_ca_label commands. Mutually exclusive with inputs:
expert
.- mris_fix_topologya unicode string
Flags to pass to mris_fix_topology commands. Mutually exclusive with inputs:
expert
.- mris_inflatea unicode string
Flags to pass to mri_inflate commands. Mutually exclusive with inputs:
expert
.- mris_make_surfacesa unicode string
Flags to pass to mris_make_surfaces commands. Mutually exclusive with inputs:
expert
.- mris_registera unicode string
Flags to pass to mris_register commands. Mutually exclusive with inputs:
expert
.- mris_smootha unicode string
Flags to pass to mri_smooth commands. Mutually exclusive with inputs:
expert
.- mris_spherea unicode string
Flags to pass to mris_sphere commands. Mutually exclusive with inputs:
expert
.- mris_surf2vola unicode string
Flags to pass to mris_surf2vol commands. Mutually exclusive with inputs:
expert
.- mrisp_painta unicode string
Flags to pass to mrisp_paint commands. Mutually exclusive with inputs:
expert
.- openmpan integer (int or long)
Number of processors to use in parallel. Maps to a command-line argument:
-openmp %d
.- parallela boolean
Enable parallel execution. Maps to a command-line argument:
-parallel
.- subject_ida unicode string
Subject name. Maps to a command-line argument:
-subjid %s
. (Nipype default value:recon_all
)- subjects_dira pathlike object or string representing an existing directory
Path to subjects directory. Maps to a command-line argument:
-sd %s
.- talairacha unicode string
Flags to pass to talairach commands. Mutually exclusive with inputs:
expert
.- use_FLAIRa boolean
Use FLAIR image to refine the pial surface. Maps to a command-line argument:
-FLAIRpial
. Mutually exclusive with inputs:use_T2
.- use_T2a boolean
Use T2 image to refine the pial surface. Maps to a command-line argument:
-T2pial
. Mutually exclusive with inputs:use_FLAIR
.- xopts‘use’ or ‘clean’ or ‘overwrite’
Use, delete or overwrite existing expert options file. Maps to a command-line argument:
-xopts-%s
.
- BA_statsa list of items which are a pathlike object or string representing an existing file
Brodmann Area statistics files.
- T1a pathlike object or string representing an existing file
Intensity normalized whole-head volume.
- annota list of items which are a pathlike object or string representing an existing file
Surface annotation files.
- aparc_a2009s_statsa list of items which are a pathlike object or string representing an existing file
Aparc a2009s parcellation statistics files.
- aparc_asega list of items which are a pathlike object or string representing an existing file
Aparc parcellation projected into aseg volume.
- aparc_statsa list of items which are a pathlike object or string representing an existing file
Aparc parcellation statistics files.
- area_piala list of items which are a pathlike object or string representing an existing file
Mean area of triangles each vertex on the pial surface is associated with.
- asega pathlike object or string representing an existing file
Volumetric map of regions from automatic segmentation.
- aseg_statsa list of items which are a pathlike object or string representing an existing file
Automated segmentation statistics file.
- avg_curva list of items which are a pathlike object or string representing an existing file
Average atlas curvature, sampled to subject.
- braina pathlike object or string representing an existing file
Intensity normalized brain-only volume.
- brainmaska pathlike object or string representing an existing file
Skull-stripped (brain-only) volume.
- curva list of items which are a pathlike object or string representing an existing file
Maps of surface curvature.
- curv_piala list of items which are a pathlike object or string representing an existing file
Curvature of pial surface.
- curv_statsa list of items which are a pathlike object or string representing an existing file
Curvature statistics files.
- entorhinal_exvivo_statsa list of items which are a pathlike object or string representing an existing file
Entorhinal exvivo statistics files.
- filleda pathlike object or string representing an existing file
Subcortical mass volume.
- graymida list of items which are a pathlike object or string representing an existing file
Graymid/midthickness surface meshes.
- inflateda list of items which are a pathlike object or string representing an existing file
Inflated surface meshes.
- jacobian_whitea list of items which are a pathlike object or string representing an existing file
Distortion required to register to spherical atlas.
- labela list of items which are a pathlike object or string representing an existing file
Volume and surface label files.
- norma pathlike object or string representing an existing file
Normalized skull-stripped volume.
- nua pathlike object or string representing an existing file
Non-uniformity corrected whole-head volume.
- origa pathlike object or string representing an existing file
Base image conformed to Freesurfer space.
- piala list of items which are a pathlike object or string representing an existing file
Gray matter/pia mater surface meshes.
- rawavga pathlike object or string representing an existing file
Volume formed by averaging input images.
- ribbona list of items which are a pathlike object or string representing an existing file
Volumetric maps of cortical ribbons.
- smoothwma list of items which are a pathlike object or string representing an existing file
Smoothed original surface meshes.
- spherea list of items which are a pathlike object or string representing an existing file
Spherical surface meshes.
- sphere_rega list of items which are a pathlike object or string representing an existing file
Spherical registration file.
- subject_ida unicode string
Subject name for whom to retrieve data.
- subjects_dira pathlike object or string representing an existing directory
Freesurfer subjects directory.
- sulca list of items which are a pathlike object or string representing an existing file
Surface maps of sulcal depth.
- thicknessa list of items which are a pathlike object or string representing an existing file
Surface maps of cortical thickness.
- volumea list of items which are a pathlike object or string representing an existing file
Surface maps of cortical volume.
- whitea list of items which are a pathlike object or string representing an existing file
White/gray matter surface meshes.
- wma pathlike object or string representing an existing file
Segmented white-matter volume.
- wmparca pathlike object or string representing an existing file
Aparc parcellation projected into subcortical white matter.
- wmparc_statsa list of items which are a pathlike object or string representing an existing file
White matter parcellation statistics file.
- property ReconAll.cmdline¶
command plus any arguments (args) validates arguments and generates command line
- ReconAll.force_run = False¶
- property ReconAll.version¶
interfaces should implement a version property
Resample¶
Bases: FSCommand
Wrapped executable:
mri_convert
.Use FreeSurfer mri_convert to up or down-sample image files
Examples
>>> from nipype.interfaces import freesurfer >>> resampler = freesurfer.Resample() >>> resampler.inputs.in_file = 'structural.nii' >>> resampler.inputs.resampled_file = 'resampled.nii' >>> resampler.inputs.voxel_size = (2.1, 2.1, 2.1) >>> resampler.cmdline 'mri_convert -vs 2.10 2.10 2.10 -i structural.nii -o resampled.nii'
- in_filea pathlike object or string representing an existing file
File to resample. Maps to a command-line argument:
-i %s
(position: -2).- voxel_sizea tuple of the form: (a float, a float, a float)
Triplet of output voxel sizes. Maps to a command-line argument:
-vs %.2f %.2f %.2f
.
- argsa unicode 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:
{}
)- resampled_filea pathlike object or string representing a file
Output filename. Maps to a command-line argument:
-o %s
(position: -1).- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- resampled_filea pathlike object or string representing an existing file
Output filename.
RobustRegister¶
Bases: FSCommand
Wrapped executable:
mri_robust_register
.Perform intramodal linear registration (translation and rotation) using robust statistics.
Examples
>>> from nipype.interfaces.freesurfer import RobustRegister >>> reg = RobustRegister() >>> reg.inputs.source_file = 'structural.nii' >>> reg.inputs.target_file = 'T1.nii' >>> reg.inputs.auto_sens = True >>> reg.inputs.init_orient = True >>> reg.cmdline 'mri_robust_register --satit --initorient --lta .../structural_robustreg.lta --mov structural.nii --dst T1.nii'References
- Reuter, M, Rosas, HD, and Fischl, B, (2010). Highly Accurate Inverse
Consistent Registration: A Robust Approach. Neuroimage 53(4) 1181-96.
- auto_sensa boolean
Auto-detect good sensitivity. Maps to a command-line argument:
--satit
. Mutually exclusive with inputs:outlier_sens
.- outlier_sensa float
Set outlier sensitivity explicitly. Maps to a command-line argument:
--sat %.4f
. Mutually exclusive with inputs:auto_sens
.- source_filea pathlike object or string representing an existing file
Volume to be registered. Maps to a command-line argument:
--mov %s
.- target_filea pathlike object or string representing an existing file
Target volume for the registration. Maps to a command-line argument:
--dst %s
.
- argsa unicode 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:
{}
)- est_int_scalea boolean
Estimate intensity scale (recommended for unnormalized images). Maps to a command-line argument:
--iscale
.- force_doublea boolean
Use double-precision intensities. Maps to a command-line argument:
--doubleprec
.- force_floata boolean
Use float intensities. Maps to a command-line argument:
--floattype
.- half_sourcea boolean or a pathlike object or string representing a file
Write source volume mapped to halfway space. Maps to a command-line argument:
--halfmov %s
.- half_source_xfma boolean or a pathlike object or string representing a file
Write transform from source to halfway space. Maps to a command-line argument:
--halfmovlta %s
.- half_targa boolean or a pathlike object or string representing a file
Write target volume mapped to halfway space. Maps to a command-line argument:
--halfdst %s
.- half_targ_xfma boolean or a pathlike object or string representing a file
Write transform from target to halfway space. Maps to a command-line argument:
--halfdstlta %s
.- half_weightsa boolean or a pathlike object or string representing a file
Write weights volume mapped to halfway space. Maps to a command-line argument:
--halfweights %s
.- high_iterationsan integer (int or long)
Max # of times on highest resolution. Maps to a command-line argument:
--highit %d
.- in_xfm_filea pathlike object or string representing an existing file
Use initial transform on source. Maps to a command-line argument:
--transform
.- init_orienta boolean
Use moments for initial orient (recommended for stripped brains). Maps to a command-line argument:
--initorient
.- iteration_thresha float
Stop iterations when below threshold. Maps to a command-line argument:
--epsit %.3f
.- least_squaresa boolean
Use least squares instead of robust estimator. Maps to a command-line argument:
--leastsquares
.- mask_sourcea pathlike object or string representing an existing file
Image to mask source volume with. Maps to a command-line argument:
--maskmov %s
.- mask_targeta pathlike object or string representing an existing file
Image to mask target volume with. Maps to a command-line argument:
--maskdst %s
.- max_iterationsan integer (int or long)
Maximum # of times on each resolution. Maps to a command-line argument:
--maxit %d
.- no_inita boolean
Skip transform init. Maps to a command-line argument:
--noinit
.- no_multia boolean
Work on highest resolution. Maps to a command-line argument:
--nomulti
.- out_reg_filea bool or None or a pathlike object or string representing a file
Registration file; either True or filename. Maps to a command-line argument:
--lta %s
. (Nipype default value:True
)- outlier_limita float
Set maximal outlier limit in satit. Maps to a command-line argument:
--wlimit %.3f
.- registered_filea boolean or a pathlike object or string representing a file
Registered image; either True or filename. Maps to a command-line argument:
--warp %s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- subsample_threshan integer (int or long)
Subsample if dimension is above threshold size. Maps to a command-line argument:
--subsample %d
.- trans_onlya boolean
Find 3 parameter translation only. Maps to a command-line argument:
--transonly
.- weights_filea boolean or a pathlike object or string representing a file
Weights image to write; either True or filename. Maps to a command-line argument:
--weights %s
.- write_vo2voxa boolean
Output vox2vox matrix (default is RAS2RAS). Maps to a command-line argument:
--vox2vox
.
- half_sourcea pathlike object or string representing an existing file
Source image mapped to halfway space.
- half_source_xfma pathlike object or string representing an existing file
Transform file to map source image to halfway space.
- half_targa pathlike object or string representing an existing file
Target image mapped to halfway space.
- half_targ_xfma pathlike object or string representing an existing file
Transform file to map target image to halfway space.
- half_weightsa pathlike object or string representing an existing file
Weights image mapped to halfway space.
- out_reg_filea pathlike object or string representing an existing file
Output registration file.
- registered_filea pathlike object or string representing an existing file
Output image with registration applied.
- weights_filea pathlike object or string representing an existing file
Image of weights used.
SegmentCC¶
Bases: FSCommand
Wrapped executable:
mri_cc
.This program segments the corpus callosum into five separate labels in the subcortical segmentation volume ‘aseg.mgz’. The divisions of the cc are equally spaced in terms of distance along the primary eigendirection (pretty much the long axis) of the cc. The lateral extent can be changed with the -T <thickness> parameter, where <thickness> is the distance off the midline (so -T 1 would result in the who CC being 3mm thick). The default is 2 so it’s 5mm thick. The aseg.stats values should be volume.
Examples
>>> from nipype.interfaces import freesurfer >>> SegmentCC_node = freesurfer.SegmentCC() >>> SegmentCC_node.inputs.in_file = "aseg.mgz" >>> SegmentCC_node.inputs.in_norm = "norm.mgz" >>> SegmentCC_node.inputs.out_rotation = "cc.lta" >>> SegmentCC_node.inputs.subject_id = "test" >>> SegmentCC_node.cmdline 'mri_cc -aseg aseg.mgz -o aseg.auto.mgz -lta cc.lta test'
- in_filea pathlike object or string representing an existing file
Input aseg file to read from subjects directory. Maps to a command-line argument:
-aseg %s
.- in_norma pathlike object or string representing an existing file
Required undocumented input {subject}/mri/norm.mgz.
- out_rotationa pathlike object or string representing a file
Global filepath for writing rotation lta. Maps to a command-line argument:
-lta %s
.- subject_ida string
Subject name. Maps to a command-line argument:
%s
(position: -1). (Nipype default value:subject_id
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- copy_inputsa boolean
If running as a node, set this to True.This will copy the input files to the node directory.
- 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
Filename to write aseg including CC. Maps to a command-line argument:
-o %s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- out_filea pathlike object or string representing a file
Output segmentation uncluding corpus collosum.
- out_rotationa pathlike object or string representing a file
Output lta rotation file.
- SegmentCC.aggregate_outputs(runtime=None, needed_outputs=None)¶
Collate expected outputs and apply output traits validation.
- SegmentCC.run(**inputs)¶
Execute this interface.
This interface will not raise an exception if runtime.returncode is non-zero.
- Parameters
cwd (specify a folder where the interface should be run) –
inputs (allows the interface settings to be updated) –
- Returns
results – A copy of the instance that was executed, provenance information and, if successful, results
- Return type
SegmentWM¶
Bases: FSCommand
Wrapped executable:
mri_segment
.This program segments white matter from the input volume. The input volume should be normalized such that white matter voxels are ~110-valued, and the volume is conformed to 256^3.
Examples
>>> from nipype.interfaces import freesurfer >>> SegmentWM_node = freesurfer.SegmentWM() >>> SegmentWM_node.inputs.in_file = "norm.mgz" >>> SegmentWM_node.inputs.out_file = "wm.seg.mgz" >>> SegmentWM_node.cmdline 'mri_segment norm.mgz wm.seg.mgz'
- in_filea pathlike object or string representing an existing file
Input file for SegmentWM. Maps to a command-line argument:
%s
(position: -2).- out_filea pathlike object or string representing a file
File to be written as output for SegmentWM. Maps to a command-line argument:
%s
(position: -1).
- argsa unicode 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:
{}
)- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- out_filea pathlike object or string representing a file
Output white matter segmentation.
Smooth¶
Bases: FSCommand
Wrapped executable:
mris_volsmooth
.Use FreeSurfer mris_volsmooth to smooth a volume
This function smoothes cortical regions on a surface and non-cortical regions in volume.
Note
Cortical voxels are mapped to the surface (3D->2D) and then the smoothed values from the surface are put back into the volume to fill the cortical ribbon. If data is smoothed with this algorithm, one has to be careful about how further processing is interpreted.
Examples
>>> from nipype.interfaces.freesurfer import Smooth >>> smoothvol = Smooth(in_file='functional.nii', smoothed_file = 'foo_out.nii', reg_file='register.dat', surface_fwhm=10, vol_fwhm=6) >>> smoothvol.cmdline 'mris_volsmooth --i functional.nii --reg register.dat --o foo_out.nii --fwhm 10.000000 --vol-fwhm 6.000000'
- in_filea pathlike object or string representing an existing file
Source volume. Maps to a command-line argument:
--i %s
.- num_itersa long integer >= 1
Number of iterations instead of fwhm. Maps to a command-line argument:
--niters %d
. Mutually exclusive with inputs:surface_fwhm
.- reg_filea pathlike object or string representing an existing file
Registers volume to surface anatomical . Maps to a command-line argument:
--reg %s
.- surface_fwhma floating point number >= 0.0
Surface FWHM in mm. Maps to a command-line argument:
--fwhm %f
. Mutually exclusive with inputs:num_iters
. Requires inputs:reg_file
.
- argsa unicode 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:
{}
)- proj_fraca float
Project frac of thickness a long surface normal. Maps to a command-line argument:
--projfrac %s
. Mutually exclusive with inputs:proj_frac_avg
.- proj_frac_avga tuple of the form: (a float, a float, a float)
Average a long normal min max delta. Maps to a command-line argument:
--projfrac-avg %.2f %.2f %.2f
. Mutually exclusive with inputs:proj_frac
.- smoothed_filea pathlike object or string representing a file
Output volume. Maps to a command-line argument:
--o %s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- vol_fwhma floating point number >= 0.0
Volume smoothing outside of surface. Maps to a command-line argument:
--vol-fwhm %f
.
- smoothed_filea pathlike object or string representing an existing file
Smoothed input volume.
SynthesizeFLASH¶
Bases: FSCommand
Wrapped executable:
mri_synthesize
.Synthesize a FLASH acquisition from T1 and proton density maps.
Examples
>>> from nipype.interfaces.freesurfer import SynthesizeFLASH >>> syn = SynthesizeFLASH(tr=20, te=3, flip_angle=30) >>> syn.inputs.t1_image = 'T1.mgz' >>> syn.inputs.pd_image = 'PD.mgz' >>> syn.inputs.out_file = 'flash_30syn.mgz' >>> syn.cmdline 'mri_synthesize 20.00 30.00 3.000 T1.mgz PD.mgz flash_30syn.mgz'
- flip_anglea float
Flip angle (in degrees). Maps to a command-line argument:
%.2f
(position: 3).- pd_imagea pathlike object or string representing an existing file
Image of proton density values. Maps to a command-line argument:
%s
(position: 6).- t1_imagea pathlike object or string representing an existing file
Image of T1 values. Maps to a command-line argument:
%s
(position: 5).- tea float
Echo time (in msec). Maps to a command-line argument:
%.3f
(position: 4).- tra float
Repetition time (in msec). Maps to a command-line argument:
%.2f
(position: 2).
- argsa unicode 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:
{}
)- fixed_weightinga boolean
Use a fixed weighting to generate optimal gray/white contrast. Maps to a command-line argument:
-w
(position: 1).- out_filea pathlike object or string representing a file
Image to write. Maps to a command-line argument:
%s
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- out_filea pathlike object or string representing an existing file
Synthesized FLASH acquisition.
UnpackSDICOMDir¶
Bases: FSCommand
Wrapped executable:
unpacksdcmdir
.Use unpacksdcmdir to convert dicom files
Call unpacksdcmdir -help from the command line to see more information on using this command.
Examples
>>> from nipype.interfaces.freesurfer import UnpackSDICOMDir >>> unpack = UnpackSDICOMDir() >>> unpack.inputs.source_dir = '.' >>> unpack.inputs.output_dir = '.' >>> unpack.inputs.run_info = (5, 'mprage', 'nii', 'struct') >>> unpack.inputs.dir_structure = 'generic' >>> unpack.cmdline 'unpacksdcmdir -generic -targ . -run 5 mprage nii struct -src .'
- configa pathlike object or string representing an existing file
Specify unpacking rules in file. Maps to a command-line argument:
-cfg %s
. Mutually exclusive with inputs:run_info
,config
,seq_config
.- run_infoa tuple of the form: (an integer (int or long), a unicode string, a unicode string, a unicode string)
Runno subdir format name : spec unpacking rules on cmdline. Maps to a command-line argument:
-run %d %s %s %s
. Mutually exclusive with inputs:run_info
,config
,seq_config
.- seq_configa pathlike object or string representing an existing file
Specify unpacking rules based on sequence. Maps to a command-line argument:
-seqcfg %s
. Mutually exclusive with inputs:run_info
,config
,seq_config
.- source_dira pathlike object or string representing an existing directory
Directory with the DICOM files. Maps to a command-line argument:
-src %s
.
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- dir_structure‘fsfast’ or ‘generic’
Unpack to specified directory structures. 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:
{}
)- log_filea pathlike object or string representing an existing file
Explicilty set log file. Maps to a command-line argument:
-log %s
.- no_info_dumpa boolean
Do not create infodump file. Maps to a command-line argument:
-noinfodump
.- no_unpack_erra boolean
Do not try to unpack runs with errors. Maps to a command-line argument:
-no-unpackerr
.- output_dira pathlike object or string representing a directory
Top directory into which the files will be unpacked. Maps to a command-line argument:
-targ %s
.- scan_onlya pathlike object or string representing an existing file
Only scan the directory and put result in file. Maps to a command-line argument:
-scanonly %s
.- spm_zeropadan integer (int or long)
Set frame number zero padding width for SPM. Maps to a command-line argument:
-nspmzeropad %d
.- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
WatershedSkullStrip¶
Bases: FSCommand
Wrapped executable:
mri_watershed
.This program strips skull and other outer non-brain tissue and produces the brain volume from T1 volume or the scanned volume.
The “watershed” segmentation algorithm was used to dertermine the intensity values for white matter, grey matter, and CSF. A force field was then used to fit a spherical surface to the brain. The shape of the surface fit was then evaluated against a previously derived template.
The default parameters are: -w 0.82 -b 0.32 -h 10 -seedpt -ta -wta
(Segonne 2004)
Examples
>>> from nipype.interfaces.freesurfer import WatershedSkullStrip >>> skullstrip = WatershedSkullStrip() >>> skullstrip.inputs.in_file = "T1.mgz" >>> skullstrip.inputs.t1 = True >>> skullstrip.inputs.transform = "transforms/talairach_with_skull.lta" >>> skullstrip.inputs.out_file = "brainmask.auto.mgz" >>> skullstrip.cmdline 'mri_watershed -T1 transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz'
- in_filea pathlike object or string representing an existing file
Input volume. Maps to a command-line argument:
%s
(position: -2).- out_filea pathlike object or string representing a file
Output volume. Maps to a command-line argument:
%s
(position: -1). (Nipype default value:brainmask.auto.mgz
)
- argsa unicode string
Additional parameters to the command. Maps to a command-line argument:
%s
.- brain_atlasa pathlike object or string representing an existing file
Maps to a command-line argument:
-brain_atlas %s
(position: -4).- 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:
{}
)- subjects_dira pathlike object or string representing an existing directory
Subjects directory.
- t1a boolean
Specify T1 input volume (T1 grey value = 110). Maps to a command-line argument:
-T1
.- transforma pathlike object or string representing a file
Undocumented. Maps to a command-line argument:
%s
(position: -3).
- out_filea pathlike object or string representing a file
Skull stripped brain volume.