Normalization of T2w/FLAIR and multiple T1w images

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.

This is normal behavior. Longitudinal analysis will not produce separate T1 images per time point, because this would make it hard to compare between time points! Instead, the longitudinal analysis flag changes how the T1 template is made. You can read more about it here.

It is not possible with fMRIPrep. T2/FLAIR images are only used by fMRIPrep to inform FreeSurfer reconstruction.

Hope this helps.