API¶
Workflows¶
fMRIprep base processing workflows¶
-
fmriprep.workflows.base.
init_fmriprep_wf
(subject_list, task_id, run_uuid, ignore, debug, low_mem, anat_only, longitudinal, omp_nthreads, skull_strip_ants, work_dir, output_dir, bids_dir, freesurfer, output_spaces, template, hires, bold2t1w_dof, fmap_bspline, fmap_demean, use_syn, force_syn, use_aroma, ignore_aroma_err, output_grid_ref)[source]¶ This workflow organizes the execution of FMRIPREP, with a sub-workflow for each subject.
If FreeSurfer is to be used, a FreeSurfer derivatives folder is created and populated with any needed template subjects.
Parameters
- subject_list : list
- List of subject labels
- task_id : str or None
- Task ID of BOLD series to preprocess, or
None
to preprocess all - run_uuid : str
- Unique identifier for execution instance
- ignore : list
- Preprocessing steps to skip (may include “slicetiming”, “fieldmaps”)
- debug : bool
- Enable debugging outputs
- low_mem : bool
- Write uncompressed .nii files in some cases to reduce memory usage
- anat_only : bool
- Disable functional workflows
- longitudinal : bool
- Treat multiple sessions as longitudinal (may increase runtime) See sub-workflows for specific differences
- omp_nthreads : int
- Maximum number of threads an individual process may use
- skull_strip_ants : bool
- Use ANTs BrainExtraction.sh-based skull-stripping workflow
If
False
, uses a faster AFNI-based workflow - work_dir : str
- Directory in which to store workflow execution state and temporary files
- output_dir : str
- Directory in which to save derivatives
- bids_dir : str
- Root directory of BIDS dataset
- freesurfer : bool
- Enable FreeSurfer surface reconstruction (may increase runtime)
- output_spaces : list
List of output spaces functional images are to be resampled to. Some parts of pipeline will only be instantiated for some output spaces.
Valid spaces:
- T1w
- template
- fsnative
- fsaverage (or other pre-existing FreeSurfer templates)
- template : str
- Name of template targeted by ‘template’ output space
- hires : bool
- Enable sub-millimeter preprocessing in FreeSurfer
- bold2t1w_dof : 6, 9 or 12
- Degrees-of-freedom for BOLD-T1w registration
- fmap_bspline : bool
- Experimental: Fit B-Spline field using least-squares
- fmap_demean : bool
- Demean voxel-shift map during unwarp
- use_syn : bool
- Experimental: Enable ANTs SyN-based susceptibility distortion correction (SDC). If fieldmaps are present and enabled, this is not run, by default.
- force_syn : bool
- Temporary: Always run SyN-based SDC
- use_aroma : bool
- Perform ICA-AROMA on MNI-resampled functional series
- ignore_aroma_err : bool
- Do not fail on ICA-AROMA errors
- output_grid_ref : str or None
- Path of custom reference image for normalization
-
fmriprep.workflows.base.
init_single_subject_wf
(subject_id, task_id, name, ignore, debug, low_mem, anat_only, longitudinal, omp_nthreads, skull_strip_ants, reportlets_dir, output_dir, bids_dir, freesurfer, output_spaces, template, hires, bold2t1w_dof, fmap_bspline, fmap_demean, use_syn, force_syn, output_grid_ref, use_aroma, ignore_aroma_err)[source]¶ This workflow organizes the preprocessing pipeline for a single subject. It collects and reports information about the subject, and prepares sub-workflows to perform anatomical and functional preprocessing.
Anatomical preprocessing is performed in a single workflow, regardless of the number of sessions. Functional preprocessing is performed using a separate workflow for each individual BOLD series.
(Source code, png, svg, pdf)
Parameters
- subject_id : str
- List of subject labels
- task_id : str or None
- Task ID of BOLD series to preprocess, or
None
to preprocess all - name : str
- Name of workflow
- ignore : list
- Preprocessing steps to skip (may include “slicetiming”, “fieldmaps”)
- debug : bool
- Enable debugging outputs
- low_mem : bool
- Write uncompressed .nii files in some cases to reduce memory usage
- anat_only : bool
- Disable functional workflows
- longitudinal : bool
- Treat multiple sessions as longitudinal (may increase runtime) See sub-workflows for specific differences
- omp_nthreads : int
- Maximum number of threads an individual process may use
- skull_strip_ants : bool
- Use ANTs BrainExtraction.sh-based skull-stripping workflow
If
False
, uses a faster AFNI-based workflow - reportlets_dir : str
- Directory in which to save reportlets
- output_dir : str
- Directory in which to save derivatives
- bids_dir : str
- Root directory of BIDS dataset
- freesurfer : bool
- Enable FreeSurfer surface reconstruction (may increase runtime)
- output_spaces : list
List of output spaces functional images are to be resampled to. Some parts of pipeline will only be instantiated for some output spaces.
Valid spaces:
- T1w
- template
- fsnative
- fsaverage (or other pre-existing FreeSurfer templates)
- template : str
- Name of template targeted by ‘template’ output space
- hires : bool
- Enable sub-millimeter preprocessing in FreeSurfer
- bold2t1w_dof : 6, 9 or 12
- Degrees-of-freedom for BOLD-T1w registration
- fmap_bspline : bool
- Experimental: Fit B-Spline field using least-squares
- fmap_demean : bool
- Demean voxel-shift map during unwarp
- use_syn : bool
- Experimental: Enable ANTs SyN-based susceptibility distortion correction (SDC). If fieldmaps are present and enabled, this is not run, by default.
- force_syn : bool
- Temporary: Always run SyN-based SDC
- output_grid_ref : str or None
- Path of custom reference image for normalization
- use_aroma : bool
- Perform ICA-AROMA on MNI-resampled functional series
- ignore_aroma_err : bool
- Do not fail on ICA-AROMA errors
Inputs
- subjects_dir
- FreeSurfer SUBJECTS_DIR
Anatomical reference preprocessing workflows¶
-
fmriprep.workflows.anatomical.
init_anat_preproc_wf
(skull_strip_ants, output_spaces, template, debug, freesurfer, longitudinal, omp_nthreads, hires, reportlets_dir, output_dir, name='anat_preproc_wf')[source]¶ This workflow controls the anatomical preprocessing stages of FMRIPREP.
This includes:
- Creation of a structural template
- Skull-stripping and bias correction
- Tissue segmentation
- Normalization
- Surface reconstruction with FreeSurfer
(Source code, png, svg, pdf)
Parameters
- skull_strip_ants : bool
- Use ANTs BrainExtraction.sh-based skull-stripping workflow.
If
False
, uses a faster AFNI-based workflow - output_spaces : list
List of output spaces functional images are to be resampled to.
Some pipeline components will only be instantiated for some output spaces.
Valid spaces:
- T1w
- template
- fsnative
- fsaverage (or other pre-existing FreeSurfer templates)
- template : str
- Name of template targeted by ‘template’ output space
- debug : bool
- Enable debugging outputs
- freesurfer : bool
- Enable FreeSurfer surface reconstruction (may increase runtime)
- longitudinal : bool
- Create unbiased structural template, regardless of number of inputs (may increase runtime)
- omp_nthreads : int
- Maximum number of threads an individual process may use
- hires : bool
- Enable sub-millimeter preprocessing in FreeSurfer
- reportlets_dir : str
- Directory in which to save reportlets
- output_dir : str
- Directory in which to save derivatives
- name : str, optional
- Workflow name (default: anat_preproc_wf)
Inputs
- t1w
- List of T1-weighted structural images
- t2w
- List of T2-weighted structural images
- subjects_dir
- FreeSurfer SUBJECTS_DIR
Outputs
- t1_preproc
- Bias-corrected structural template, defining T1w space
- t1_brain
- Skull-stripped
t1_preproc
- t1_mask
- Mask of the skull-stripped template image
- t1_seg
- Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)
- t1_tpms
- List of tissue probability maps in T1w space
- t1_2_mni
- T1w template, normalized to MNI space
- t1_2_mni_forward_transform
- ANTs-compatible affine-and-warp transform file
- t1_2_mni_reverse_transform
- ANTs-compatible affine-and-warp transform file (inverse)
- mni_mask
- Mask of skull-stripped template, in MNI space
- mni_seg
- Segmentation, resampled into MNI space
- mni_tpms
- List of tissue probability maps in MNI space
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
- fs_2_t1_transform
- Affine transform from FreeSurfer subject space to T1w space
- surfaces
- GIFTI surfaces (gray/white boundary, midthickness, pial, inflated)
Subworkflows
-
fmriprep.workflows.anatomical.
init_skullstrip_ants_wf
(debug, omp_nthreads, name='skullstrip_ants_wf')[source]¶ This workflow performs skull-stripping using ANTs’
BrainExtraction.sh
(Source code, png, svg, pdf)
Parameters
- debug : bool
- Enable debugging outputs
- omp_nthreads : int
- Maximum number of threads an individual process may use
Inputs
- in_file
- T1-weighted structural image to skull-strip
Outputs
- bias_corrected
- Bias-corrected
in_file
, before skull-stripping - out_file
- Skull-stripped
in_file
- out_mask
- Binary mask of the skull-stripped
in_file
- out_report
- Reportlet visualizing quality of skull-stripping
Surface preprocessing¶
fmriprep
uses FreeSurfer to reconstruct surfaces from T1w/T2w
structural images.
-
fmriprep.workflows.anatomical.
init_surface_recon_wf
(omp_nthreads, hires, name='surface_recon_wf')[source]¶ This workflow reconstructs anatomical surfaces using FreeSurfer’s
recon-all
.Reconstruction is performed in three phases. The first phase initializes the subject with T1w and T2w (if available) structural images and performs basic reconstruction (
autorecon1
) with the exception of skull-stripping. For example, a subject with only one session with T1w and T2w images would be processed by the following command:$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -i <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T1w.nii.gz \ -T2 <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T2w.nii.gz \ -autorecon1 \ -noskullstrip
The second phase imports an externally computed skull-stripping mask. The final phase resumes reconstruction, using the T2w image to assist in finding the pial surface, if available. See
init_autorecon_resume_wf()
for details.(Source code, png, svg, pdf)
Parameters
- omp_nthreads : int
- Maximum number of threads an individual process may use
- hires : bool
- Enable sub-millimeter preprocessing in FreeSurfer
Inputs
- t1w
- List of T1-weighted structural images
- t2w
- List of T2-weighted structural images (only first used)
- skullstripped_t1
- Skull-stripped T1-weighted image (or mask of image)
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
Outputs
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
- fs_2_t1_transform
- FSL-style affine matrix translating from FreeSurfer T1.mgz to T1w
- surfaces
- GIFTI surfaces for gray/white matter boundary, pial surface, midthickness (or graymid) surface, and inflated surfaces
- out_report
- Reportlet visualizing quality of surface alignment
Subworkflows
-
fmriprep.workflows.anatomical.
init_autorecon_resume_wf
(omp_nthreads, name='autorecon_resume_wf')[source]¶ This workflow resumes recon-all execution, assuming the -autorecon1 stage has been completed.
In order to utilize resources efficiently, this is broken down into five sub-stages; after the first stage, the second and third stages may be run simultaneously, and the fourth and fifth stages may be run simultaneously, if resources permit:
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -autorecon2-volonly $ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -autorecon-hemi lh \ -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 \ -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg \ -noapas2aseg -nosegstats -nowmparc -nobalabels $ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -autorecon-hemi rh \ -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 \ -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg \ -noapas2aseg -nosegstats -nowmparc -nobalabels $ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -autorecon3 -hemi lh -T2pial $ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -autorecon3 -hemi rh -T2pial
The excluded steps in the second and third stages (
-no<option>
) are not fully hemisphere independent, and are therefore postponed to the final two stages.(Source code, png, svg, pdf)
Inputs
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
- use_T2
- Refine pial surface using T2w images
Outputs
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
- out_report
- Reportlet visualizing quality of surface alignment
-
fmriprep.workflows.anatomical.
init_gifti_surface_wf
(name='gifti_surface_wf')[source]¶ This workflow prepares GIFTI surfaces from a FreeSurfer subjects directory
If midthickness (or graymid) surfaces do not exist, they are generated and saved to the subject directory as
lh/rh.midthickness
. These, along with the gray/white matter boundary (lh/rh.smoothwm
), pial sufaces (lh/rh.pial
) and inflated surfaces (lh/rh.inflated
) are converted to GIFTI files. Additionally, the vertex coordinates arerecentered
to align with native T1w space.(Source code, png, svg, pdf)
Inputs
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
Outputs
- surfaces
- GIFTI surfaces for gray/white matter boundary, pial surface, midthickness (or graymid) surface, and inflated surfaces
BOLD fMRI -processing workflows¶
-
fmriprep.workflows.bold.
init_func_preproc_wf
(bold_file, ignore, freesurfer, bold2t1w_dof, reportlets_dir, output_spaces, template, output_dir, omp_nthreads, fmap_bspline, fmap_demean, use_syn, force_syn, use_aroma, ignore_aroma_err, debug, low_mem, output_grid_ref, layout=None)[source]¶ This workflow controls the functional preprocessing stages of FMRIPREP.
(Source code, png, svg, pdf)
Parameters
- bold_file : str
- BOLD series NIfTI file
- ignore : list
- Preprocessing steps to skip (may include “slicetiming”, “fieldmaps”)
- freesurfer : bool
- Enable FreeSurfer functional registration (bbregister) and resampling BOLD series to FreeSurfer surface meshes.
- bold2t1w_dof : 6, 9 or 12
- Degrees-of-freedom for BOLD-T1w registration
- reportlets_dir : str
- Directory in which to save reportlets
- output_spaces : list
List of output spaces functional images are to be resampled to. Some parts of pipeline will only be instantiated for some output spaces.
Valid spaces:
- T1w
- template
- fsnative
- fsaverage (or other pre-existing FreeSurfer templates)
- template : str
- Name of template targeted by ‘template’ output space
- output_dir : str
- Directory in which to save derivatives
- omp_nthreads : int
- Maximum number of threads an individual process may use
- fmap_bspline : bool
- Experimental: Fit B-Spline field using least-squares
- fmap_demean : bool
- Demean voxel-shift map during unwarp
- use_syn : bool
- Experimental: Enable ANTs SyN-based susceptibility distortion correction (SDC). If fieldmaps are present and enabled, this is not run, by default.
- force_syn : bool
- Temporary: Always run SyN-based SDC
- use_aroma : bool
- Perform ICA-AROMA on MNI-resampled functional series
- ignore_aroma_err : bool
- Do not fail on ICA-AROMA errors
- debug : bool
- Enable debugging outputs
- low_mem : bool
- Write uncompressed .nii files in some cases to reduce memory usage
- output_grid_ref : str or None
- Path of custom reference image for normalization
- layout : BIDSLayout
- BIDSLayout structure to enable metadata retrieval
Inputs
- bold_file
- BOLD series NIfTI file
- t1_preproc
- Bias-corrected structural template image
- t1_brain
- Skull-stripped
t1_preproc
- t1_mask
- Mask of the skull-stripped template image
- t1_seg
- Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)
- t1_tpms
- List of tissue probability maps in T1w space
- t1_2_mni_forward_transform
- ANTs-compatible affine-and-warp transform file
- t1_2_mni_reverse_transform
- ANTs-compatible affine-and-warp transform file (inverse)
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
- fs_2_t1_transform
- Affine transform from FreeSurfer subject space to T1w space
Outputs
- bold_t1
- BOLD series, resampled to T1w space
- bold_mask_t1
- BOLD series mask in T1w space
- bold_mni
- BOLD series, resampled to template space
- bold_mask_mni
- BOLD series mask in template space
- confounds
- TSV of confounds
- surfaces
- BOLD series, resampled to FreeSurfer surfaces
- aroma_noise_ics
- Noise components identified by ICA-AROMA
- melodic_mix
- FSL MELODIC mixing matrix
-
fmriprep.workflows.bold.
init_bold_reference_wf
(omp_nthreads, bold_file=None, name='bold_reference_wf')[source]¶ This workflow generates reference BOLD images for a series
The raw reference image is the target of HMC, and a contrast-enhanced reference is the subject of distortion correction, as well as boundary-based registration to T1w and template spaces.
(Source code, png, svg, pdf)
Parameters
- bold_file : str
- BOLD series NIfTI file
- omp_nthreads : int
- Maximum number of threads an individual process may use
- name : str
- Name of workflow (default:
bold_reference_wf
)
Inputs
- bold_file
- BOLD series NIfTI file
Outputs
- bold_file
- Validated BOLD series NIfTI file
- raw_ref_image
- Reference image to which BOLD series is motion corrected
- skip_vols
- Number of non-steady-state volumes detected at beginning of
bold_file
- ref_image
- Contrast-enhanced reference image
- ref_image_brain
- Skull-stripped reference image
- bold_mask
- Skull-stripping mask of reference image
- bold_mask_report
- Reportlet showing quality of masking
- validation_report
- HTML reportlet indicating whether
bold_file
had a valid affine
-
fmriprep.workflows.bold.
init_bold_hmc_wf
(metadata, bold_file_size_gb, ignore, name='bold_hmc_wf', omp_nthreads=1)[source]¶ This workflow performs HMC over the input BOLD image.
(Source code, png, svg, pdf)
Parameters
- metadata : dict
- BIDS metadata for BOLD file
- bold_file_size_gb : float
- Size of BOLD file in GB
- ignore : list
- Preprocessing steps to skip - if “slicetiming” is included, skip slice-timing correction
- name : str
- Name of workflow (default:
bold_hmc_wf
) - omp_nthreads : int
- Maximum number of threads an individual process may use
Inputs
- bold_file
- BOLD series NIfTI file
- raw_ref_image
- Reference image to which BOLD series is motion corrected
- skip_vols
- Number of non-steady-state volumes detected at beginning of
bold_file
Outputs
- bold_split
- Individual 3D volumes, not motion corrected
- xforms
- List of affine transforms aligning each volume to
ref_image
in ITK format - movpar_file
- MCFLIRT motion parameters, normalized to SPM format (X, Y, Z, Rx, Ry, Rz)
-
fmriprep.workflows.bold.
init_bold_reg_wf
(freesurfer, bold2t1w_dof, bold_file_size_gb, name='bold_reg_wf', use_compression=True, use_fieldwarp=False)[source]¶ This workflow registers the reference BOLD image to T1-space, using a boundary-based registration (BBR) cost function.
If FreeSurfer-based preprocessing is enabled, the
bbregister
utility is used to align the BOLD images to the reconstructed subject, and the resulting transform is adjusted to target the T1 space. If FreeSurfer-based preprocessing is disabled, FSL FLIRT is used with the BBR cost function to directly target the T1 space.(Source code, png, svg, pdf)
Parameters
- freesurfer : bool
- Enable FreeSurfer functional registration (bbregister)
- bold2t1w_dof : 6, 9 or 12
- Degrees-of-freedom for BOLD-T1w registration
- bold_file_size_gb : float
- Size of BOLD file in GB
- name : str
- Name of workflow (default:
bold_reg_wf
) - use_compression : bool
- Save registered BOLD series as
.nii.gz
- use_fieldwarp : bool
- Include SDC warp in single-shot transform from BOLD to T1
Inputs
- name_source
- BOLD series NIfTI file Used to recover original information lost during processing
- ref_bold_brain
- Reference image to which BOLD series is aligned
If
fieldwarp == True
,ref_bold_brain
should be unwarped - ref_bold_mask
- Skull-stripping mask of reference image
- t1_preproc
- Bias-corrected structural template image
- t1_brain
- Skull-stripped
t1_preproc
- t1_mask
- Mask of the skull-stripped template image
- t1_seg
- Segmentation of preprocessed structural image, including gray-matter (GM), white-matter (WM) and cerebrospinal fluid (CSF)
- bold_split
- Individual 3D BOLD volumes, not motion corrected
- hmc_xforms
- List of affine transforms aligning each volume to
ref_image
in ITK format - subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
- fs_2_t1_transform
- Affine transform from FreeSurfer subject space to T1w space
- fieldwarp
- a DFM in ITK format
Outputs
- mat_bold_to_t1
- Affine transform from
ref_bold_brain
to T1 space (FSL format) - mat_t1_to_bold
- Affine transform from T1 space to BOLD space (FSL format)
- itk_bold_to_t1
- Affine transform from
ref_bold_brain
to T1 space (ITK format) - itk_t1_to_bold
- Affine transform from T1 space to BOLD space (ITK format)
- bold_t1
- Motion-corrected BOLD series in T1 space
- bold_mask_t1
- BOLD mask in T1 space
- fs_reg_file
- Affine transform from
ref_bold_brain
to T1 space (FreeSurferreg
format) - out_report
- Reportlet visualizing quality of registration
Registration workflows¶
-
fmriprep.workflows.util.
init_bbreg_wf
(bold2t1w_dof, report, reregister=True, name='bbreg_wf')[source]¶ This workflow uses FreeSurfer’s
bbregister
to register a BOLD image to a T1-weighted structural image.It is a counterpart to
init_fsl_bbr_wf()
, which performs the same task using FSL’s FLIRT with a BBR cost function.(Source code, png, svg, pdf)
Parameters
- bold2t1w_dof : 6, 9 or 12
- Degrees-of-freedom for BOLD-T1w registration
- report : bool
- Generate visual report of registration quality
- rereigster : bool, optional
- Update affine registration matrix with FreeSurfer-T1w transform (default: True)
- name : str, optional
- Workflow name (default: bbreg_wf)
Inputs
- in_file
- Reference BOLD image to be registered
- fs_2_t1_transform
- FSL-style affine matrix translating from FreeSurfer T1.mgz to T1w
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID (must have folder in SUBJECTS_DIR)
- t1_brain
- Unused (see
init_fsl_bbr_wf()
) - t1_seg
- Unused (see
init_fsl_bbr_wf()
)
Outputs
- out_matrix_file
- FSL-style registration matrix
- out_reg_file
- FreeSurfer-style registration matrix (.dat)
- final_cost
- Value of cost function at final registration
- out_report
- reportlet for assessing registration quality
-
fmriprep.workflows.util.
init_fsl_bbr_wf
(bold2t1w_dof, report, name='fsl_bbr_wf')[source]¶ This workflow uses FSL FLIRT to register a BOLD image to a T1-weighted structural image, using a boundary-based registration (BBR) cost function.
It is a counterpart to
init_bbreg_wf()
, which performs the same task using FreeSurfer’sbbregister
.Parameters
- bold2t1w_dof : 6, 9 or 12
- Degrees-of-freedom for BOLD-T1w registration
- report : bool
- Generate visual report of registration quality
- name : str, optional
- Workflow name (default: fsl_bbr_wf)
Inputs
- in_file
- Reference BOLD image to be registered
- t1_brain
- Skull-stripped T1-weighted structural image
- t1_seg
- FAST segmentation of
t1_brain
- fs_2_t1_transform
- Unused (see
init_bbreg_wf()
) - subjects_dir
- Unused (see
init_bbreg_wf()
) - subject_id
- Unused (see
init_bbreg_wf()
)
Outputs
- out_matrix_file
- FSL-style registration matrix
- out_reg_file
- Unused (see
init_bbreg_wf()
) - final_cost
- Value of cost function at final registration
- out_report
- reportlet for assessing registration quality
Resampling workflows¶
-
fmriprep.workflows.bold.
init_bold_surf_wf
(output_spaces, name='bold_surf_wf')[source]¶ This workflow samples functional images to FreeSurfer surfaces
For each vertex, the cortical ribbon is sampled at six points (spaced 20% of thickness apart) and averaged.
Outputs are in GIFTI format.
(Source code, png, svg, pdf)
Parameters
- output_spaces : list
- List of output spaces functional images are to be resampled to
Target spaces beginning with
fs
will be selected for resampling, such asfsaverage
or related template spaces If the list containsfsnative
, images will be resampled to the individual subject’s native surface
Inputs
- source_file
- Motion-corrected BOLD series in T1 space
- subjects_dir
- FreeSurfer SUBJECTS_DIR
- subject_id
- FreeSurfer subject ID
Outputs
- surfaces
- BOLD series, resampled to FreeSurfer surfaces
-
fmriprep.workflows.bold.
init_bold_mni_trans_wf
(template, bold_file_size_gb, name='bold_mni_trans_wf', output_grid_ref=None, use_compression=True, use_fieldwarp=False)[source]¶ This workflow samples functional images to the MNI template in a “single shot” from the original BOLD series.
(Source code, png, svg, pdf)
Parameters
- template : str
- Name of template targeted by ‘template’ output space
- bold_file_size_gb : float
- Size of BOLD file in GB
- name : str
- Name of workflow (default:
bold_mni_trans_wf
) - output_grid_ref : str or None
- Path of custom reference image for normalization
- use_compression : bool
- Save registered BOLD series as
.nii.gz
- use_fieldwarp : bool
- Include SDC warp in single-shot transform from BOLD to MNI
Inputs
- itk_bold_to_t1
- Affine transform from
ref_bold_brain
to T1 space (ITK format) - t1_2_mni_forward_transform
- ANTs-compatible affine-and-warp transform file
- bold_split
- Individual 3D volumes, not motion corrected
- bold_mask
- Skull-stripping mask of reference image
- name_source
- BOLD series NIfTI file Used to recover original information lost during processing
- hmc_xforms
- List of affine transforms aligning each volume to
ref_image
in ITK format - fieldwarp
- a DFM in ITK format
Outputs
- bold_mni
- BOLD series, resampled to template space
- bold_mask_mni
- BOLD series mask in template space
Utility workflows¶
-
fmriprep.workflows.util.
init_enhance_and_skullstrip_bold_wf
(name='enhance_and_skullstrip_bold_wf', omp_nthreads=1)[source]¶ This workflow takes in a BOLD volume, and attempts to enhance the contrast between gray and white matter, and skull-stripping the result.
(Source code, png, svg, pdf)
Inputs
- in_file
- BOLD image (single volume)
Outputs
- bias_corrected_file
- the
in_file
after N4BiasFieldCorrection - skull_stripped_file
- the
bias_corrected_file
after skull-stripping - mask_file
- mask of the skull-stripped input file
- out_report
- reportlet for the skull-stripping
-
fmriprep.workflows.util.
init_skullstrip_bold_wf
(name='skullstrip_bold_wf')[source]¶ This workflow applies skull-stripping to a BOLD image.
It is intended to be used on an image that has previously been bias-corrected with
init_enhance_and_skullstrip_bold_wf()
(Source code, png, svg, pdf)
Inputs
- in_file
- BOLD image (single volume)
Outputs
- skull_stripped_file
- the
in_file
after skull-stripping - mask_file
- mask of the skull-stripped input file
- out_report
- reportlet for the skull-stripping