I want to extract clusters within the cortical lesion mask in which the vertex values are below 49.95
The values are in the file lh.MS075_R01_07_R1year.subjspace.mgh Thanks, Vale ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> Sent: Monday, May 20, 2019 2:46:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with mri_surfcluster How did you choose thresholds of 1 and 49.95? In general, you don't need to set --thmax. If you input is a binary mask, then you should set --thmin to somethiing below 1 (eg, 0.5) On 5/20/19 2:40 PM, Barletta, Valeria wrote: > > Dear Freesurfers, > > I am trying to obtain clusters of vertices whit a certain value over a > threshold inside a lesion mask projected to the surface, with the command: > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mask > lh.surf_magn_CL02_fwhm1.mgh --thmax 49.95807 --thmin 1 --sign pos > --minarea 0.01 --sum summary.txt > > But I obtain this result saying there are no vertices in my mask. > > thsign = pos, id = 1 > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ > hemi = lh > srcid = > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/CME_all/lh.MS075_R01_07_R1year.subjspace.mgh > > srcsubjid = MS075_R01_07_R1year > srcsurf = lh.pial > srcframe = 0 > thsign = pos > thmin = 1 > thmax = 49.9581 > fdr = -1 > minarea = 0.01 > xfmfile = talairach.xfm > nth = -1 > sumfile = > /autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/49_subjects/SINGLE_LESION/MS075_R01_07_R1year/summary.txt > subjectsdir = > /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 > FixMNI = 1 > Found 0 vertices in mask > > > Can you help me figure out why? > > Thanks, > Vale > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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