Thanks - I very much appreciate your thorough explanation!

We don't expect changes in the actual structure of the brain, but I am concerned about alignment of the structure in 3D space within the scanner. You're probably aware that when using software like FSL, it is typically advisable to align a functional image to a structural image taken in the same session. To my knowledge, this is because the software needs the high-resolution information in the structural image at the same position to correctly identify the position of the functional image in the same space.

Could you confirm Freesurfer should be able to identify and align functional image even with a T1 from a different session where, for example, the subject's position in the scanner differs by several centimeters from one session to the next?

On Tue, Feb 20, 2018 at 2:09 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

If you are combining the T1 images together in recon-all, then it is not
possible to separate them in FSFAST. If you do not expect structural
changes, then you can just register both fMRI sessions to the single
anatomical. If you are expecting changes, then analyze the T1 images
separately (in the longitudinal stream). This creates two subject names;
use the appropriate one in each fmri session.

On 02/16/2018 02:30 AM, Ben Smith wrote:
> (Thanks for your feedback to my previous inquiry - I've resolved this
> problem)
>
> I'm running FsFastPreProc on a dataset with a number of
> subjects, where each subject has two sessions.
>
> There's a separate structural image taken in each session. I want to
> make sure each subject's functional data is registered to the correct
> structural image. When running fsfast, setting up the file structure I
> can see clearly how FsFast uses the subjectname file to identify the
> right subject. It also seems easy enough to register multiple T1
> images - just include multiple inputs for each subject to the
> *recon-all* command.
>
> But how do I map the session to the appropriate T1 image in the
> structural data?
>
> Also, if I were registering feat directories to structural using
> reg-feat2anat - how would I specify the session in that case?
>
> Does this even matter? Perhaps FSFastPreProc is built to process
> images without having a T1 from the same session as each image.
>
> If there's not an easy way to do this, would a suitable workaround be
> to create a separate anatomical subject folder for every subject*session?
>
> Thanks very much for your help!
>
> Best regards
>
> Ben
>
>
> _______________________
> Ben Smith, MSc.
> Ph.D. Candidate
> University of Southern California
> https://bjsmith.github.io/
> w | +1 213-740 7851
> m | +1 323-385 9349
> skype | ben.smith.nz <http://ben.smith.nz/>
>
>
>
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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