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