Provide outputfiles for fMRIPrep to replace recon-all pipeline by T1Prep

[ChristianGaser]

Files after running fmriprep with recon-all in anat:

already prepared:

• sub-01_desc-brain_mask.json
• sub-01_desc-brain_mask.nii.gz
• sub-01_desc-preproc_T1w.json
• sub-01_desc-preproc_T1w.nii.gz
• sub-01_dseg.nii.gz
• sub-01_label-CSF_probseg.nii.gz
• sub-01_label-GM_probseg.nii.gz
• sub-01_label-WM_probseg.nii.gz
• sub-01_hemi-L_curv.shape.gii
• sub-01_hemi-L_midthickness.surf.gii
• sub-01_hemi-L_pial.surf.gii
• sub-01_hemi-L_sphere.surf.gii
• sub-01_hemi-L_sulc.shape.gii
• sub-01_hemi-L_thickness.shape.gii
• sub-01_hemi-L_white.surf.gii
• sub-01_hemi-L_inflated.surf.gii
• sub-01_hemi-L_desc-cortex_mask.label.gii
• sub-01_hemi-R_curv.shape.gii
• sub-01_hemi-R_midthickness.surf.gii
• sub-01_hemi-R_pial.surf.gii
• sub-01_hemi-R_sphere.surf.gii
• sub-01_hemi-R_sulc.shape.gii
• sub-01_hemi-R_thickness.shape.gii
• sub-01_hemi-R_white.surf.gii
• sub-01_hemi-R_inflated.surf.gii
• sub-01_hemi-R_desc-cortex_mask.label.gii

prepared, but not yet working

• sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
• sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
• sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
• sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
• sub-01_desc-ribbon_mask.json
• sub-01_desc-ribbon_mask.nii.gz
  convert_h5_transform_precision

unclear how difficult it will be

• sub-01_desc-aparcaseg_dseg.nii.gz
• sub-01_desc-aseg_dseg.nii.gz
• sub-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
• sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
• sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
• sub-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
• sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
• sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii

Files after running fmriprep with recon-all in func:

• sub-01_task-listen_run-01_desc-brain_mask.json
• sub-01_task-listen_run-01_desc-brain_mask.nii.gz
• sub-01_task-listen_run-01_desc-confounds_timeseries.json
• sub-01_task-listen_run-01_desc-confounds_timeseries.tsv
• sub-01_task-listen_run-01_desc-coreg_boldref.json
• sub-01_task-listen_run-01_desc-coreg_boldref.nii.gz
• sub-01_task-listen_run-01_desc-hmc_boldref.json
• sub-01_task-listen_run-01_desc-hmc_boldref.nii.gz
• sub-01_task-listen_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
• sub-01_task-listen_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
• sub-01_task-listen_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
• sub-01_task-listen_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
• sub-01_task-listen_run-01_space-MNI152NLin2009cAsym_boldref.json
• sub-01_task-listen_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
• sub-01_task-listen_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
• sub-01_task-listen_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
• sub-01_task-listen_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
• sub-01_task-listen_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz