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 _______________________________________________ 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.
