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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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Issues in final preprocessing run #3317

Open NeuroJo-RA opened 5 days ago

NeuroJo-RA commented 5 days ago

What happened?

I'm very new to fmriprep. I followed a tutorial to have it installed with docker and then after running our BIDS formatted data, i didn't receive any images. I used ezBIDS to format the raw data from the scan. I could really use some guidance on anything that you all could tell me about where I went wrong.

crash-20240624-203327-root-rotime-84ae02c3-66b0-41cd-9d14-3b36da1df16e.txt

What command did you use?

#User inputs:
bids_root_dir=$HOME/Downloads/bids2
subj=01
nthreads=4
mem=20 #gb
container=docker 

#Begin:

#Convert virtual memory from gb to mb
mem=`echo "${mem//[!0-9]/}"` #remove gb at end
mem_mb=`echo $(((mem*1000)-5000))` #reduce some memory for buffer space during pre-processing

#export TEMPLATEFLOW_HOME=$HOME/.cache/templateflow
export FS_LICENSE=$HOME/Downloads/freesurferlicense.txt

#Run fmriprep
  fmriprep-docker $bids_root_dir $bids_root_dir/derivatives \
    participant \
    --participant-label $subj \
    --skip-bids-validation \
    --md-only-boilerplate \
    --fs-license-file $HOME/Downloads/license.txt \
    --fs-no-reconall \
    --output-spaces MNI152NLin2009cAsym:res-2 \
    --nthreads $nthreads \
    --stop-on-first-crash \
    --mem_mb $mem_mb

What version of fMRIPrep are you running?

fMRIPrep 23.2.3

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response

tsalo commented 5 days ago

It looks like your field maps or BOLD scans are missing the PhaseEncodingDirection metadata field. For what it's worth, the validator would probably catch that for you, since it's a recommended field for BOLD data and required for PEPOLAR-style field maps. If you don't absolutely have to, I'd recommend dropping --skip-bids-validation when you run fMRIPrep.

NeuroJo-RA commented 5 days ago

Great! I'll drop the skip from the bash file. Could you tell me where I could acquire the PhaseEncodingDirection metadata field? Is that something that I enter manually or is it acquired at the time of the scan? Sorry, if that's very obvious information.

tsalo commented 5 days ago

It's typically extracted from the DICOMs and added automatically to the JSON files by dcm2niix (or whatever dicom-to-nifti conversion tool you use). You can find it in the DICOMs if you have them, or the protocol PDF (at least for Siemens scans).