New subject: FsFastPreProc Registration of files from each session to their session's structural image

20 Feb 2018

      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/
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m | +1 323-385 9349
skype | ben.smith.nz http://ben.smith.nz/

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Re: [Freesurfer] FsFastPreProc Registration of files from each session to their session's structural image