fMRIPrep not saving BOLD output file

Software Support
1

Summary of what happened:

After running fMRIPrep v20.2.3 one BOLD file is not written as output.
In our nifti directory (which houses the BIDS converted data) the Inductivemoney run2 is there.

However, after running fMRIPrep, the output for Inductivemoney run 2 is not written.

I noticed in the work flow directory there are some outputs missing for run 2 for this participant: (image shows run 1 vs run 2)

image
image797×327 135 KB

Question: Is there another log file to find that may have helpful error information? Alternatively, does anything here stand out as to why the preproc BOLD file for run 2 is not being written?

Many thanks in advance for your guidance and input!
–khwood

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep --work-dir $dataset_dir/workdir/ \
         --participant-label $pid \
         --output-spaces T1w \
         --fs-license-file /data/project/NLSB/Data/license.txt \
         --n-cpus 4 \
         --omp-nthreads 4 \
         --cifti-output 91k \
         $bidsdir \
         $bidsdir/derivatives \
         participant

Version:

20.2.3

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

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

This is one error message within the slurm job output:

Standard error:
Exception caught during reference file reading 

itk::ImageFileReaderException (0x2317840)
Location: "unknown" 
File: /src/ants/build/staging/include/ITK-5.1/itkImageFileReader.hxx
Line: 133
Description:  Could not create IO object for reading file /data/project/NLSB/Data/SAMI/UCLA_SAMI_SCANS/workdir/fmriprep_wf/single_subject_SAMI16123_wf/func_preproc_task_Inductivemoney_run_2_wf/bold_split/vol0178.nii.gz
  Tried to create one of the following:
    BMPImageIO
    BioRadImageIO
    Bruker2dseqImageIO
    GDCMImageIO
    GE4ImageIO
    GE5ImageIO
    GiplImageIO
    HDF5ImageIO
    JPEGImageIO
    JPEG2000ImageIO
    LSMImageIO
    MGHImageIO
    MINCImageIO
    MRCImageIO
    MetaImageIO
    NiftiImageIO
    NrrdImageIO
    PNGImageIO
    StimulateImageIO
    TIFFImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Screenshots / relevant information:

2

Hi @khwood and welcome to neurostars!

In the future please use the Software Support post template. You can see I edited it back in for you this time, and that there is still information missing. Importantly, this includes the BIDS validator output, and computational environment. If not using a container, I recommend using a container, and updating to the most recent version (24.1.1 at this time). How much resources are you giving to the job?

Best,
Steven

3

Hi Steven,

Thank you for adding back the missing text (this is my first post and I was not sure if that text was to be included or deleted…)

The environment I’m using is a high-performance computing platform that does not require a container to run fMRIPrep.

Summary of BIDS validator is as follows:

bids-validator@1.4.0

[32mThis dataset appears to be BIDS compatible.[39m

        [34m[4mSummary:[24m[39m                  [34m[4mAvailable Tasks:[24m[39m                                    [34m[4mAvailable Modalities:[24m[39m 
        848 Files, 74.34GB        Inductivemoney                                      T1w                   
        17 - Subjects             Inductivesocial                                     T2w                   
        1 - Session               Perceptualnonsocial                                 bold                  
                                  Perceptualsocial                                    events                
                                  banditMoney                                         sbref                 
                                  banditSocial                                        fieldmap              
                                  implicitNonsocial                                                         
                                  implicitSocial                                                            
                                  TODO: full task name for Inductivemoney                                   
                                  TODO: full task name for Inductivesocial                                  
                                  TODO: full task name for Perceptualnonsocial                              
                                  TODO: full task name for Perceptualsocial                                 
                                  TODO: full task name for banditMoney                                      
                                  TODO: full task name for implicitNonsocial                                
                                  TODO: full task name for banditSocial                                     
                                  TODO: full task name for implicitSocial                                   

[36m	If you have any questions, please post on https://neurostars.org/tags/bids.[39m

We are using v20.2.3 because the rest of the participants for this study have been preprocessed with this version…

I am giving 1 node and 6 cores as resources to support the job.

Thank you again!
–khwood

4

Hi @khwood,

I would still recommend using a container. How much RAM are you giving? Does the error persist on a fresh working directory or updated version?

Best,
Steven

5

Hi Steven,

The RAM is 10GB per CPU with 6 CPUs running. Have not tried a fresh working directory! Will give that a shot. Thank you!

Please let me know if you think of any other ideas or places I can look for errors, etc.

Many thanks,
–khwood

6

Hi @khwood,

It’s possible that 10GB is not enough if there are 8 different tasks (and perhaps multiple runs of certain tasks).

Best,
Steven