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 wi…

Hi @Shahar_Ben_Noun , You did not include MNI as an output space in your fmriprep command. Best, Steven

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

@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.

@Steven Alright :)) Thank you so much!

[image] No (aparc+)aesg output from fmriprep Software Support This probably got lost in the refactor. What spaces were they resampled into? I can’t remember off the top of my head where they used to go. They are pretty easy to pull out of FreeSurfer, though. H…

@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 …

Hi, I actually came back to this matter. Thanks to the replies I got in this thread I’m no longet stuck at the matter, but I still don’t get - Why doesn’t fMRIPrep create desc-aparcaseg_dseg files automatically as it used to? Am I missing an input when running fMRIPrep?

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

Software Support

effigies May 14, 2024, 9:07pm 8

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