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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
