Q1. I have been using smriprep to process T1w images normalized to MNI space. Participants of my data underwent multiple sessions with 1~2 runs each. Since I want to analyze data longitudinally, I want fmriprep to process my T1w images independently. However, what I get is one processed T1w images per one subject. What should I do? I have attached the code I used below.
> docker run --rm -e DOCKER_VERSION_8395080871=20.10.12 -it -v /home/bjy0614/license.txt:/opt/freesurfer/license.txt:ro -v /home/bjy0614/share/oasis/oasis_mri_script/oasis_mri_files/sub-OAS30001:/data:ro -v /home/bjy0614/share/oasis/oasis_mri_script/oasis_mri_files/sub-OAS30001/ses-d0129/anat/test4:/out nipreps/smriprep:0.8.2 --nprocs 32 --longitudinal --output-spaces MNI152NLin2009cAsym --skull-strip-mode force --fs-no-reconall /data /out participant
Q2. My data set also includes T2w and FLAIR images. Is it possible to normalize T2w and FLAIR images into MNI space with fmriprep?
Thank you.