Just run funcroi-sess without specifying a contrast or -vol. Alternatively, you can just specify -map cespct and it will give the percent change.
doug Adam Nitenson wrote: > Hi Freesurfers, > > When conducting ROI analyses in Stable 5, is there a way to generate > a mean functional baseline offset value within the ROI which can be > used to help calculate percent signal change? This would correspond > to the value from row 4 in the output file generated by > roisummary-sess in Stable 4. > > Thanks, > > Adam > > > PS: Here are examples of the commands I've used in Stable 5 to generate > ROI Data: > > funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi > MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs -thresh 1.3 > > funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -sf > /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH > > funcroi-table-sess -roi MTH_7vFix_DLPFC.roicfg -sf > /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH > -c Cond7vFix -o /cluster/roffman/users/Stable5_PerRun/DLPFC_ROI_7vFix_MTH > > > > > >> You need to specify a threshold (-thresh) with a contrast. This is the >> equivalent to the -min in funcroi-sess. There was a bug in >> funcroi-config that prevented it from catching that you did not specify >> a threshold (which has been fixed now). >> thanks >> doug >> >> Adam Nitenson wrote: >> >>> Hi Freesurfers, >>> >>> I'm trying to analyze functional data in Stable 5, but have noticed >>> that the func2roi command is no longer used. My analysis involves 9 >>> conditions (not including Fixation) and 1 timepoint for each. The >>> steps I used in Stable 4 to generate this data are as follows: >>> >>> func2roi-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals >>> -anatlabel LH_16MTH_7v1_DLPFC -sf >>> /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped >>> -d >>> /cluster/roffman/users/MTH_Study >>> >>> roisummary-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals >>> -sf >>> /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped >>> -d >>> /cluster/roffman/users/MTH_Study -sumfile >>> /cluster/roffman/users/MTH_Study/ROI_Analysis/LH_16MTH_7v1Label_DLPFC >>> >>> In Stable 5, I see that there are several commands, funcroi-config, >>> funcroi-sess, and funcroi-table-sess. Looking at other threads, it seems >>> like I need to make a roicfg file for each contrast. So far I have >>> tried: >>> >>> funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi >>> MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs >>> >>> and then >>> >>> funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -sf >>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH >>> >>> ...but for the latter, I get the following error: >>> PVF (null) >>> Thesholding hit volume. >>> done >>> mri_binarize --i >>> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/Cond7vFix/sig.nii >>> --frame 0 --mask >>> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii >>> --o >>> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii >>> --abs --min >>> ERROR: --min flag needs 1 argument >>> >>> I don't see the --min argument described for either funcroi-config or >>> funcroi-sess, so I was wondering what I needed to add/change to generate >>> data similar to what I did for Stable 4. >>> >>> >>> Thanks, >>> >>> Adam Nitenson, B.S. >>> Brain Genomics Lab >>> Massachusetts General Hospital >>> niten...@nmr.mgh.harvard.edu >>> Phone: 617-643-3215 >>> _______________________________________________ >>> 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 >> >> >> >> > > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > niten...@nmr.mgh.harvard.edu > Phone: 617-643-3215 > _______________________________________________ > 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.
