Missing FreeSurfer functional and anatomical derivatives using existing SUBJECTS_DIR

[Steven]

Hi @dgfitch and welcome to neurostars!

@dgfitch

sub-<subject_label>_[specifiers]_space-T1w_desc-aparcaseg_dseg.nii.gz
sub-<subject_label>_[specifiers]_space-T1w_desc-aseg_dseg.nii.gz

See below:

No (aparc+)aesg output from fmriprep

This probably got lost in the refactor. What spaces were they resampled into? I can’t remember off the top of my head where they used to go. They are pretty easy to pull out of FreeSurfer, though. Here you can resample in MNI with a particular BOLD run to ensure that your voxels align with that run: mri_convert sourcedata/freesurfer/sub-XYZ/mri/aseg.{mgz,nii.gz} antsApplyTransforms \ -i sourcedata/freesurfer/sub-XYZ/mri/aseg.nii.gz \ -r sub-XYZ/func/sub-XYZ_task-TASK_space-MNI152NLin20…

@dgfitch

• • sub-<subject_label>_[specifiers]_hemi-[LR]_space-<space_label>_bold.func.gii

You need to use a FreeSurfer output space for these (fsnative, fsaverage, etc)

@dgfitch

• • sub-<subject_label>[_space-<space_label>]_desc-preproc_T2w.nii.gz

Are you sure those subjects had T2 images? Can you replicate this in most recent release (24.0.1 at this time)?

Best,
Steven