fMRIPREP registration issue for single run

Finally I managed to set up your data and I made it all the way through for several sessions. Later today I’ll be able to check on that run that was off.

Okay, now that I have my eyes on your data I realized of a detail in the “About” section of your report:


  • FMRIPrep version: 1.3.2
  • FMRIPrep command: /usr/local/miniconda/bin/fmriprep /scratch/users/coreyf/HSR /scratch/users/coreyf/HSR/preprocessed participant --participant_label sub-25 --output-space T1w template --fs-license-file /scratch/users/coreyf/license.txt -w /tmp/work --nthreads 10 --omp-nthreads 1 --longitudinal -vvv --skip_bids_validation
  • Date preprocessed: 2019-04-10 22:24:48 -0700

Have you tried without --skip_bids_validation? - Your dataset is not BIDS Valid and I’m surprised how fMRIPrep made it that far for you. I’m going to run overwriting the metadata, but that might be the culprit.

ha! and another one - it is fine if you want to store your results under the original data folder, but BIDS prescribes a derivatives/ folder to do so. So, instead of:

fmriprep /scratch/users/coreyf/HSR /scratch/users/coreyf/HSR/preprocessed

please use something along the lines of BIDS-Derivatives recommendations:

fmriprep /scratch/users/coreyf/HSR /scratch/users/coreyf/HSR/derivatives/fmriprep-1.3.2

Therefore, I add the derivatives/ folder that will be hanging from the BIDS root and under that I recommend to collect your processing and analysis following the recommendation of derivatives/<pipeline_name>-<version>/

Hi Corey, I could not replicate your problems with fMRIPrep-1.5.0. The only large difference is that I couldn’t run fieldmap corrections since the metadata did not contain the IntendedFor field.

Hi Oscar,

The json files I uploaded to google drive in the fmap folders contain the “IntendedFor” field. Other than switching fMRIPREP versions and not running the fieldmap correction, was anything else changed (ie, the call to fMRIPREP, any optional arguments,etc)?