Hi FreeSurfer team,

I am running a 3 day experiment and want to concatenate my data in time. Thus, I’ve been trying to transform my data such that voxel indices from all my sessions/days line up (subject’s head is in the scanner slightly differently on each day).

First, I created a 3D Motion Correction template for each day (i.e. MCTemplate1.nii.gz, MCTemplate2.nii.gz, MCTemplate3.nii.gz) and aligned each template to a FreeSurfer orig.mgz manually (because the anatomy comes from a different session):

tkregister2 --s bert --mov MCTemplate1.nii.gz --regheader-center --reg manreg_day1.dat

Then I used bbregister for finetuning the alignment bbregister:

bbregister --s bert --mov MCTemplate1.nii.gz --reg autoreg_day1.dat --init-reg manreg_day1.dat --bold --o bboutput_day1.nii.gz

So I end up with 3 registration matrices (.dat) that map between the 3 functional volumes and the 1 anatomy. I also have 3 nifti files of the functional volumes that have been resampled into the anatomical space. When I open these in fslview (open one, add the others) they are all aligned and sharing voxel indices as I want, but they are also oriented wrongly, and too big (for the sake of analysis speed later on I want to keep functional data in its original size). The same nifti's output with the --no-resample flag do not overlay once viewed with fslview.

I could describe all the other things I have tried but that would make this a very long message (i.e. saving out the regheader matrices and concatenating with those, inverting the transformations and using flirt to apply those, etc. etc.). My hope is someone has figured this out before and could tell me the correct steps.

Pointers would be much appreciated! -Rosanne