Re: [Freesurfer] Func2ROI in Stable 4 --> FuncROI in Stable 5

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 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