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
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.
