Hello,
I'm getting started with freesurfer. I've played around with some of
the tutorial data for fs-fast
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was
able to follow along and successfully carry out the preprocessing
exercises (which sufficed for my purposes), which also included running
register-sess on the "rest" tutorial data for sess01.
I've run into a few gotchas with some resting state data, and wanted to
know if there are any problems specific to processing resting state data
that can be easily avoided?
For example, here's the file structure:
Project root:
/home/chris/resting
Anatomical data root ($SUBJECTS_DIR):
/home/chris/resting/anat
Functional data root ($FUNCTIONALS_DIR):
/home/chris/resting/func
Subject 1 anatomical directory:
$SUBJECTS_DIR/sub00156
(already run through recon-all)
Subject 1 functional directory:
$FUNCTIONALS_DIR/sub00156
contains:
subjectname ("sub00156")
and a nii file in a nested subdirectory:
$FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz
Where f.nii.gz is some resting state data (hence no paradigm files)
For my inaugural attempt, I've run anatomical data for a participant
through recon-all, and was having problems registering
$FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in
$SUBJECTS_DIR/sub00156. After some trial and error and wandering through
this mailing list, I found I had to first run mktemplate-sess and then
register-sess (the fs-fast tutorial lead me to believe everything was
automatically handled by preproc-sess). Are these deviations a
foreseeable consequence of working with resting state data? Is there
some documentation of important considerations for working with resting
state data?
Thanks for any help,
Chris
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