Hi Chris, it should have been done with preproc-sess. What was your preproc-sess command line? At some point, I had it set up so that it would go to the bold directory by default unless you used "-fsd rest". Newer versions require you to specify the FSD specifically.
doug
On 11/5/12 9:38 PM, Chris McNorgan wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer