qsiprep.workflows.dwi.fsl module

Implementing the FSL preprocessing workflow

qsiprep.workflows.dwi.fsl.init_fsl_hmc_wf(scan_groups, source_file, t2w_sdc, dwi_metadata=None, slice_quality='outlier_n_sqr_stdev_map', name='fsl_hmc_wf')

This workflow controls the dwi preprocessing stages using FSL tools.

I couldn’t get this to work reliably unless everything was oriented in LAS+ before going to TOPUP and eddy. For this reason, if TOPUP is going to be used (for an epi fieldmap or an RPE series) or there is no fieldmap correction, operations occurring before eddy are done in LAS+. The fieldcoefs are applied during eddy’s run and the corrected series comes out. This is finally converted to LPS+ and sent to the rest of the pipeline.

If a GRE fieldmap is available, the correction is applied to eddy’s outputs after they have been converted back to LPS+.

Finally, if SyN is chosen, it is applied to the LPS+ converted, eddy-resampled data.

Parameters

scan_groups: dict

dictionary with fieldmaps and warp space information for the dwis

impute_slice_threshold: float

threshold for a slice to be replaced with imputed values. Overrides the parameter in eddy_config if set to a number > 0.

pepolar_methodstr

Either ‘DRBUDDI’, ‘TOPUP’ or ‘DRBUDDI+TOPUP’. The method for SDC when EPI fieldmaps are used.

eddy_config: str

Path to a JSON file containing settings for the call to eddy.

Inputs

dwi_file: str

DWI series. Possibly concatenated, denoised, etc

bvec_file: str

bvec file

bval_file: str

bval file

json_file: str

path to sidecar json file for dwi_file

b0_indices: list

Indexes into dwi_files that correspond to b=0 volumes

b0_images: list

List of single b=0 volumes

original_files: list

List of the files from which each DWI volume came. One per original file

t1_brain: str

Skull stripped T1w image

t1_mask: str

mask for t1_brain

qsiprep.workflows.dwi.fsl.init_fsl_hmc_wf(scan_groups, source_file, t2w_sdc, dwi_metadata=None, slice_quality='outlier_n_sqr_stdev_map', name='fsl_hmc_wf')

This workflow controls the dwi preprocessing stages using FSL tools.

I couldn’t get this to work reliably unless everything was oriented in LAS+ before going to TOPUP and eddy. For this reason, if TOPUP is going to be used (for an epi fieldmap or an RPE series) or there is no fieldmap correction, operations occurring before eddy are done in LAS+. The fieldcoefs are applied during eddy’s run and the corrected series comes out. This is finally converted to LPS+ and sent to the rest of the pipeline.

If a GRE fieldmap is available, the correction is applied to eddy’s outputs after they have been converted back to LPS+.

Finally, if SyN is chosen, it is applied to the LPS+ converted, eddy-resampled data.

Parameters

scan_groups: dict

dictionary with fieldmaps and warp space information for the dwis

impute_slice_threshold: float

threshold for a slice to be replaced with imputed values. Overrides the parameter in eddy_config if set to a number > 0.

pepolar_methodstr

Either ‘DRBUDDI’, ‘TOPUP’ or ‘DRBUDDI+TOPUP’. The method for SDC when EPI fieldmaps are used.

eddy_config: str

Path to a JSON file containing settings for the call to eddy.

Inputs

dwi_file: str

DWI series. Possibly concatenated, denoised, etc

bvec_file: str

bvec file

bval_file: str

bval file

json_file: str

path to sidecar json file for dwi_file

b0_indices: list

Indexes into dwi_files that correspond to b=0 volumes

b0_images: list

List of single b=0 volumes

original_files: list

List of the files from which each DWI volume came. One per original file

t1_brain: str

Skull stripped T1w image

t1_mask: str

mask for t1_brain