Location of Transformation Files for Longitudinal Processing

Hello everyone!

I wanted to ask a quick question about how fMRIprep saves its transformation files. For the project I ran, I processed 1 subject who had 4 different scanning sessions where a T1 anatomic image and functional data were captured at each session. For the subject folder, these scans are organized as “ses-1, ses-2, ses-3, and ses-4.” From my understand after looking at the fMRIprep workflow, the T1s from sessions 2, 3, and 4 are aligned to the T1 from session 1, and it is that final alignment of all 4 T1s that is normalized. Therefore, the final .h5 transformation file in the “sub-54/anat” directory would be able to transform any images in session 1’s native space to MNI space, but this same transformation would not work for any images in the native spaces of sessions 2, 3, and 4 since they were aligned with session 1 before normalization.

What I am wondering is if the transformation files from the alignment of sessions 2, 3, and 4 is saved anywhere? If I wanted to move masks from the native spaces of sessions 2, 3, and 4, I would have to first apply the transformation from the alignments of these sessions into template space, then I could apply the h5 transformation. However, I do not know where the transformation files to put them into template space are located, or if they exist at all.

Any assistance would be greatly appreciated. Thank you for reading.