Dear experts,
Our dataset have two time points (sessions) per subject and for each session it has a T1w image. We are interested to run freesurfer’s longitudinal pipeline via smriprep, which would essentially do all 3 steps in the longitudinal routine of freesurfer i.e. cross-sectional run for each time point, base/template creation stage, and finally the longitudinal stage where it would robustly coregister individual time points to the base/template space. Is this possible via smriprep?
I tried running smriprep 0.6.1 with longitudinal flag, however it did not give output as expected. It just created one subject folder within the output folder like “~/derivatives/freesurfer/sub-abc/{label,mri,scripts,stats,surf,tmp,touch,trash}”. What output files did this folder contain, was it in the average t1 space from both the time points, or did it just pull T1 for one of sessions?
What does longitudinal flag exactly do, is there a detailed documentation anywhere about its usage?
Thank you,
Sneha