Support surface-based fMRI processing

[HippocampusGirl]

These workflows need updating. May also be a good opportunity to add targeted unit tests for different input file formats (NIfTI, CIFTI, TSV) and docstrings.

Resampling to the surface

• Factory for the resampling to MNI152NLin6Asym
• Factory for bold_surf_wf to fsaverage and fsnative
• workflow and Factory for MSM
• Factory for bold_grayords_wf

Quality checks

• anat_reports_wf add SurfaceSnapshots
• anat_reports_wf add segmentation render as per ENIGMA QC manual
• halfpipe.workflow.report needs to pass through the surface-based reports images to the reports folder

Postprocessing workflows

• halfpipe.workflow.setting.bandpassfilter init_bandpass_filter_wf
• halfpipe.workflow.setting.confounds init_confounds_regression_wf
• halfpipe.workflow.setting.fmriprepadapter needs to also get the CIFTI files from fMRIPrep
• halfpipe.workflow.setting.grandmeanscaling init_grand_mean_scaling_wf
• halfpipe.workflow.setting.icaaroma init_ica_aroma_regression_wf
• halfpipe.workflow.setting.settingadapter needs to support multiple BOLD outputs
• halfpipe.workflow.setting.smoothing init_smoothing_wf

Feature extraction

• halfpipe.workflow.feature.atlasbasedconnectivity
• halfpipe.workflow.feature.dualregression
• halfpipe.workflow.feature.falff
• halfpipe.workflow.feature.reho
• halfpipe.workflow.feature.seedbasedconnectivity
• halfpipe.workflow.feature.taskbased

Group model

• halfpipe.workflow.model.base

Nice to have

• Import existing FreeSurfer and match subject IDs

[HippocampusGirl]

Justification