Hi folks,
I have a question regarding the output format of the fmriprep docker image. Here is the command I used:
docker run --rm -e DOCKER_VERSION_8395080871=24.0.2 -it --memory=15g -v C:\Users\myaccount\Documents\retinotopy-dataset\freesurfer.txt:/opt/freesurfer/license.txt:ro -v C:\Users\myaccount\Documents\retinotopy-dataset:/data:ro -v C:\Users\myaccount\Documents\retinotopy-dataset\output:/out poldracklab/fmriprep:latest /data /out participant --participant-label PVTS102 --output-spaces fsaverage --low-mem
The results were generated in .gii format. However, when I ran the same command with the default “output-spaces,” the results were in .nii.gz format. I noticed that some people have their fmriprep results in .mgz format. I would like to know if fmriprep provides an option to obtain the results in the desired format, or if I need to use a conversion command in freesurfer to convert them to .mgz?
Thank you for your help.