Desc-aparcaseg_dseg.nii.gz and MNI files missing after running fMRIprep

Hi everyone, I’d appreciate your help regrading trouble I’m having with fMRIprep

Summary of what happened:

I ran the minimal level version of fMRIprep and was missing the files of the templates such as “sub-01_desc-aparcaseg_dseg.nii” and “sub-01_desc-aseg_dseg.nii”

I thought it might has to do with me running it in its minimal version so I tried running it again at full version but the problem recurred and even more concerning, I realized I don’t have the MNI transformed files either - no “sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii”

Command used

singularity run -B /ems/elsc-labs/benyakov-a/Lab-Shared/BIDS_data/06_05_24_pilot/ -B /ems/elsc-labs/benyakov-a/Lab-Shared/collab_projects/2nd_run/imaging/ -B /usr/local/freesurfer/7.3.2/ --cleanenv /opt/ct/fmriprep_23.2.1.sif /ems/elsc-labs/benyakov-a/Lab-Shared/BIDS_data/06_05_24_pilot/ /ems/elsc-labs/benyakov-a/Lab-Shared/collab_projects/2nd_run/fmriprep_output participant -w /ems/elsc-labs/benyakov-a/Lab-Shared/collab_projects/2nd_run/imaging/fmriprep_work --fs-license-file /usr/local/freesurfer/7.3.2/license.txt --output-space T1w --nthreads 9 --participant-label 01 02 03

I thought this is rather unexpected as I got a message saying “fMRIPrep finished successfully!” and checking the html report I see no errors occured.

Thanks in advance!
Shahar


Hi @Shahar_Ben_Noun,

You did not include MNI as an output space in your fmriprep command.

Best,
Steven

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If I understood correctly the documentation at fmriprep version documentation fMRIPrep uses MNI152NLin2009cAsym as standardization reference by default, why wasn’t it the case now?

Also, will putting MNI in output space create the desc-aparcaseg_dseg.nii as well?

Thanks for the swift reply!

Hi @Shahar_Ben_Noun,

It is the default, but by specifying your own output space you override the default.

Best,
Steven

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@Steven

That makes perfect sense, thanks!

Will putting MNI in output space create the desc-aparcaseg_dseg.nii files as well?

I would think that would come just from using FreeSurfer, but it’s worth a shot.

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@Steven Alright :))
Thank you so much!

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@effigies Thanks! fMRIPrep is still re-running and hopefully it’ll be solved now but if not I’ll be sure to check out your solution :slight_smile:

Continuing the discussion from Desc-aparcaseg_dseg.nii.gz and MNI files missing after running fMRIprep:

Summary of what happened:

In before, when I ran fMRIPrep it had automatically created files such

fmriprep_output\sub-01\anat\sub-01_desc-aparcaseg_dseg.nii.gz

For some reason it longer creates these files, at least not by default.
Why doesn’t it do it automatically as it used to? Does anyone know about an arguement I’m missing when running fMRIPrep?

Command used

 singularity run -B /{path}/BIDS_data/06_05_24_pilot/  -B /{path}/06_05_24_pilot/imaging/ 
-B /{path}/freesurfer/7.3.2/ --cleanenv /opt/ct/fmriprep_23.2.1.sif  /{path}/BIDS_data/06_05_24_pilot/ 
 /{path}/06_05_24_pilot/fmriprep_output  participant -w /{path}/06_05_24_pilot/imaging/fmriprep_work 
--fs-license-file /{path}/freesurfer/7.3.2/license.txt --output-space T1w MNI152NLin2009cAsym --nthreads 9 
--participant-label 01 02 03 --slice-time-ref 0

**Many thanks to @‘effigies’ who helped me find an older thread about converting the .mgz files to nifti in this post, allowing me to continue my work in the meantime