fMRIPrep Normalization failed in a problematic subject

Software Support
1

Summary of what happened:

fMRIPrep was successfully finished for this subject, but the normalization is not right. I knew something was wrong with this subject as our scanning note indicated: “hippocampal tilt was applied to fieldmap - normalization might be off”. However problems with the field map should not affect T1 normalization.
Is there any chance that this subject could be saved? We had a particular task with a longitudinal design, and each subject is invaluable to our study.
dropbox link for bids
[Dropbox](https://dropbox link for fmriprep results)

Version:

23.2.1

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

Screenshots / relevant information:

image
image1920×934 212 KB

image
image1920×646 70 KB

2

The brain mask failed, rather than the normalization. Find some other way to create a brain mask, and then store it as a derivative in the way fMRIPrep would:

mymask/
  sub-XYZ/
    anat/
      sub-XYZ_desc-brain_mask.nii.gz

Then pass that directory with --derivatives:

fmriprep $BIDS_DIR $FMRIPREP_DIR participant $FLAGS --derivatives $MYMASK
3

Thanks! Glad that I can bring this subject back. However, the --derivatives didn’t work.

I put the mask under following path (the same way with the bids for this subject):
test/aProblemmaticSubject/mask/sub-LM002/ses-T1/anat/sub-LM002_ses-T1_desc-brain_mask.nii.gz
then I run:

fmriprep-docker test/aProblemmaticSubject/bids      test/aProblemmaticSubject/fmriprep 
--participant-label  sub-LM002 
--work-dir test/aProblemmaticSubject/fmriprep/workD 
--fs-license-file /usr/local/freesurfer/7.4.1/license.txt 
--write-graph 
--output-spaces T1w MNI152NLin2009cAsym fsaverage fsaverage5 
--derivatives test/aProblemmaticSubject/mask

without the --derivatives, it had no problem, with “–derivatives test/aProblemmaticSubject/mask”
error message like this:

Traceback (most recent call last):
  File "/home/dcnladmin/toolbox/fsl/bin/fmriprep-docker", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/dcnladmin/toolbox/fsl/lib/python3.11/site-packages/fmriprep_docker/__main__.py", line 420, in main
    opts, unknown_args = parser.parse_known_args()
                         ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/dcnladmin/toolbox/fsl/lib/python3.11/argparse.py", line 1902, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/dcnladmin/toolbox/fsl/lib/python3.11/argparse.py", line 2114, in _parse_known_args
    start_index = consume_optional(start_index)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/dcnladmin/toolbox/fsl/lib/python3.11/argparse.py", line 2054, in consume_optional
    take_action(action, args, option_string)
  File "/home/dcnladmin/toolbox/fsl/lib/python3.11/argparse.py", line 1978, in take_action
    action(self, namespace, argument_values, option_string)
  File "/home/dcnladmin/toolbox/fsl/lib/python3.11/site-packages/fmriprep_docker/__main__.py", line 266, in __call__
    k, v = kv.split("=")
    ^^^^
ValueError: not enough values to unpack (expected 2, got 1)
5

Figured out. the flag should be --derivatives mymask=/path/to/mymask
Thank you!