Hi, I am using fmriprep v. 1.3.2. The wierd thing is that fmriprep doesn’t save T2 images in output folder, and saves only one file of 3: sub-1_desc-preproc_T1w.nii.gz
Here is a tree of BIDS directory
/tmp/BIDS/
├── CHANGES
├── README
├── dataset_description.json
├── participants.json
├── participants.tsv
├── sub-1
│ ├── anat
│ │ ├── sub-1_T1MprageSagP2IsoOrig_T1w.json
│ │ ├── sub-1_T1MprageSagP2IsoOrig_T1w.nii.gz
│ │ ├── sub-1_T2SpaceDaFlCorP2IsoOrig_FLAIR.json
│ │ ├── sub-1_T2SpaceDaFlCorP2IsoOrig_FLAIR.nii.gz
│ │ ├── sub-1_T2SpaceNsTra06MmIso_T2w.json
│ │ └── sub-1_T2SpaceNsTra06MmIso_T2w.nii.gz
│ ├── sub-1_scans.json
│ └── sub-1_scans.tsv
And fmriprep output is only mprage series:
logs
│ ├── CITATION.bib
│ ├── CITATION.html
│ ├── CITATION.md
│ └── CITATION.tex
├── sub-1
│ └── anat
│ ├── sub-1_T1MprageSagP2IsoOrig_from-orig_to-T1w_mode-image_xfm.txt
│ ├── sub-1_desc-preproc_T1w.json
│ ├── sub-1_desc-preproc_T1w.nii.gz
│ └── sub-1_from-T1w_to-fsnative_mode-image_xfm.txt
freesurfer output mri have only orig in t2:
mri
│ ├── T1.mgz
│ ├── brainmask.auto.mgz
│ ├── brainmask.mgz
│ ├── ctrl_pts.mgz
│ ├── mri_nu_correct.mni.log
│ ├── mri_nu_correct.mni.log.bak
│ ├── norm.mgz
│ ├── nu.mgz
│ ├── orig
│ │ ├── 001.mgz
│ │ └── T2raw.mgz
│ ├── orig.mgz
│ ├── orig_nu.mgz
│ ├── rawavg.mgz
│ ├── talairach.label_intensities.txt
│ ├── talairach.log
I have thought that the issue is coming from of --skip-bids-validation
flag, however naming of files is according to BIDS specification:
sub-control01
○ anat
■ sub-control01_T1w.nii.gz
■ sub-control01_T1w.json
■ sub-control01_T2w.nii.gz
■ sub-control01_T2w.json