FMRI Prep and Slice Time Correction

Hi @ChrisGorgolewski

Thanks for that. Below are the answers to your questions.

OS: Centos 7, kernel: 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Docker version: Singularity version 3.0.1 was used to convert the Docker image of fMRIPrep (version 1.2.5)

shell script: had directories and the following commands:

module load fmriprep/1.2.5

Run fmriprep

–participant-label ${subject}
–output-space {T1w,template}
–mem_mb 80000
-n-cpus 8
–fs-license-file ${fslicense}
-w ${workdir}

Hi, just wanted to state that I’m having the same issue. I’m running fmriprep on a supercomputer with 100GB alloted for one participant (pilot testing, too), and I’m getting the same error. Any updates on this?

I experience the same error (during the call to Bids Validator) with the docker fmriprep version 1.2.4 and 1.2.5 (1.2.3 runs fine) on Ubuntu 16.04.5 LTS, on a machine with 32Gb of RAM, even with a small dataset (one participant from the YALE-trt dataset)

PS: using option --skip-bids-validation, docker fmriprep 1.2.5 runs fine, hence the issue is definitely with the BIDS validator

@jcrdubois @pettitta - any chance you could share a small dataset that consistently triggers this issue for you?

I sent you a message with a link to the dataset. Please let me know if you need anything else!

ETA: I’ve also run using fmriprep 1.2.5 and 1.2.4 and the only way to get it to work for both versions is to add the --skip_bids_validation

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I fixed the issue by fixing a naming error: the bold files were named sub-{}_ses-{}_run-{}_task-rest_bold.nii.gz instead of sub-{}_ses-{}_task-{}_run-{}_bold.nii.gz, which meant they did not comply with the BIDS specification.
It thus appears that the BIDS validator crashes with an out-of-memory error in versions 1.2.4 and 1.2.5 in some cases when the data is not BIDS compliant?
I can send you the original, offending data if it is useful, let me know.

@jcrdubois thanks for this. I will try this and keep you guys posted :slight_smile:

Hi @jcrdubois

I’ve gone through the BIDS spec doc again, and tried adding in “run-1” and / or “ses-1” to my naming system but I kept running into the same memory error. I’ve attached examples below.

Also, is there a way you could share a screen shot showing how you’ve named your ME-files?

Example with no run or ses number:


Run and ses number added:


Thank you for your help. I’m still learning the ropes with ME-data and fMRI in general and all your replies are very much appreciated.


Could you try using the standalone validator ( with the environment variable



Hi @TribikramT my files are named exactly like I specified above,


(it is not ME data – I realize that this thread was originally about ME data)

Does your data pass the online BIDS validator without errors now? In my case, v 1.2.4 and 1.2.5 crashed when my data was not BIDS compliant. This is an issue to look into and fix (@ChrisGorgolewski should I open an issue on github for this?), but in the meantime you should ensure your data is BIDS compliant and hopefully you won’t run into the memory error.


There is an issue about this error already open

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Hi All,

Just an update.

fMRI Prep was able to run with no memory error and STC was applied. I relocated the files to a simple folder structure (tree structure: <project_name> - - <[rawdata] [derivatives] [temp]>) instead of <project_name> - - <pilot_testing> - -<fmriprep_versions> - -<sub_ID> - -<[rawdata] [derivatives] [temp]>.

I am not sure why this approach solved the issue. However, fMRIPrep v1.2.5 now works on my ME-data. Yay! :slight_smile:

The way I was able to determine this solution was by first finding out in what folder structure the BIDS validator worked (web version and command line version). Once, I determined where it worked, I redirected the fMRI Prep script to work off data in that folder, and it worked! :slight_smile:

Thank you very much for your help. Much appreciated.


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