I am trying to run fMRIPrep on my n-back data using pre-run FreeSurfer outputs, but it does not work correctly because I realized that it does not use the FreeSurfer outputs and always crashes during autorecon. I have read that is still working on longitudinal data however I can’t use it as well as cross sectional.
ERROR: It appears that this subject ID is an existing
base/template from longitudinal processing (-base):
sub-101
If you are trying to re-run a -base template you
need to pass the -base and all -tp flags:
\' -base -tp ... -all \'
(Instead of -all you can pass other flags, such
as -autorecon2 -autorecon3 to run only parts.)
Stderr:
Traceback:
RuntimeError: subprocess exited with code 1.
I have read many issues here, but after trying some options, none of them work.
-1st option. Use my data as longitudinal with this issue: Add --fs-no-resume option to reuse existing freesurfer outputs without resuming (eg. longitudinal pipeline base) by bpinsard · Pull Request #393 · nipreps/smriprep · GitHub but this aprouch was not recognice by fmripre.
fmriprep /home/user/neurodesktop-storage/Agueda/BIDS/derivatives/fmriprep7 /home/user/neurodesktop-storage/Agueda/BIDS/derivatives/fmriprep7/derivatives/fmriprep participant -longitudinal --participant-label sub-101 --skip_bids_validation --fs-reuse-base -v --fs-license-file /home/user/neurodesktop-storage/Agueda/BIDS/derivatives/fmriprep7/license.txt --fs-subjects-dir [/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/freesurfer/outputs
-2nd option. Adding the freesurfer directory with --fs-subjects-dir but trying to use my pre-run freesurfer outputs as cross sectional data but it still give me the same error with autorecon.
fmriprep /home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/fmriprep_long] /home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/fmriprep_long/derivatives/fmriprep](https://colab.research.google.com/drive/1JjDqHG6TfY6zyWryfh57T6vKOZCiuVmI?hl=es#) participant --participant-label sub-101 --skip_bids_validation -v --skull-strip-t1w force --fs-license-file [/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/fmriprep_long/license.txt --fs-subjects-dir [/home/jovyan/neurodesktop-storage/Agueda/BIDS/derivatives/freesurfer/outputs
I have try to reorganice my freesurfer folder in differents ways but is not working anyway.
I guess the issue could be that the fs recon-all was ran with a older version of freesurfer so may I can’t use it.The fmirprep version that I am using is 23.2.1 and freesurfer version was 7.4.1 .
Thanks so much