Currently, it is not as convenient to do this with version 5. You have to create a condition-vs-fixation for each condition that you want a time course for. Then for each condition, you need to run funcroi-table-sess for each time point (using the -frame option), then construct the waveforms from these files. It's a bit of a hassle, but scriptable.
doug Yuko Yotsumoto wrote: > Hi All, > > I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 > > I'd like to plot HDR for each condition for each subject. > With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess. > > With v5.0, those commands do not seem to work. > > I could get a table with: >> funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi >> lh.DLPFC.roicfg -contrast all_null -sign abs -thresh 1 -force >> funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 >> funcroi-table-sess -o >> /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt >> >> -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh -c all_null > > However, what I want is BOLD values in each time point for all conditions. > funcroi-table-sess fails if I do not specify a contrast. > >> funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi >> lh.DLPFC.roicfg -force >> funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 >> funcroi-table-sess -o >> /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan/ROIs/lh_DLPFC/lh_DLPFC_VM20.txt >> >> -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 -a VMfwhm5lh > > ERROR: must specify a contrast > > Is there a command that gives me values, not a table? > > Thank you, > Yuko > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
