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 generatea 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 noticedthat 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 nitenson@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 greve@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 nitenson@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