For my own understanding, because this seems to have happened on every single one of the subjects in a large dataset, but the fMRIprep outputs look fine. Does the bids-validator require something different than fMRIprep for files? I thought initially this might have been related to this or this, but it looks like these were resolved long before I ran into this, and none of these files are symlinked. This is using fMRIprep
1-4-1rc5, for continuity with other parts of this large dataset processed with this version.
Edit: I noticed after combing through the logs a bit more that this did not happen with the first several hundred subjects in a given BIDS dir, but then occurred consistently for everyone afterwards. Wondering if it actually is related to the issue above with not closing the files or something, because my logs do end abruptly with
OSError: handle is closed and
ulimit -Hn gives 4096 as expected.
I get an error during BIDS validation for every subject about
1: [ERR] We were unable to read this file. Make sure it contains data (file size > 0 kB) and is not corrupted, incorrectly named, or incorrectly symlinked. (code: 44 - FILE_READ) ./sub-NDARINVGBXJFCXY/anat/sub-NDARINVGBXJFCXY_run-01_T1w.nii.gz ./sub-NDARINVGBXJFCXY/dwi/sub-NDARINVGBXJFCXY_run-01_dwi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-dMRI_dir-AP_run-04_epi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-dMRI_dir-PA_run-03_epi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-02_epi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-06_epi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-08_epi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-10_epi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-12_epi.nii.gz ./sub-NDARINVGBXJFCXY/fmap/sub-NDARINVGBXJFCXY_acq-fMRI_dir-PA_run-01_epi.nii.gz ... and 8 more files having this issue (Use --verbose to see them all).
However, fMRIprep continues and runs fine, and I get all the expected outputs. They were converted with Heudiconv. This happens both with files with lenient permissions and those that were converted by another user that are read-only. Is it something weird with Singularity and symlinks?
./fmap: total 8408 -rwxrwxr-x 1 utooley mackey_group 24138 Jul 22 19:03 sub-NDARINVGBXJFCXY_acq-dMRI_dir-AP_run-04_epi.json -rwxrwxr-x 1 utooley mackey_group 1518323 Jul 18 09:23 sub-NDARINVGBXJFCXY_acq-dMRI_dir-AP_run-04_epi.nii.gz -rwxrwxr-x 1 utooley mackey_group 24135 Jul 22 19:03 sub-NDARINVGBXJFCXY_acq-dMRI_dir-PA_run-03_epi.json -rwxrwxr-x 1 utooley mackey_group 1509001 Jul 18 09:23 sub-NDARINVGBXJFCXY_acq-dMRI_dir-PA_run-03_epi.nii.gz -rwxrwxr-x 1 utooley mackey_group 18530 Jul 22 19:03 sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-02_epi.json -rwxrwxr-x 1 utooley mackey_group 534005 Jul 18 09:23 sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-02_epi.nii.gz -rwxrwxr-x 1 utooley mackey_group 18534 Jul 22 19:03 sub-NDARINVGBXJFCXY_acq-fMRI_dir-AP_run-06_epi.json
Log file attached.
log.txt (909.3 KB)