And what about the mask? Display the mask in freeview at a threshold of 0.5
On 5/20/19 3:09 PM, Barletta, Valeria wrote: > > This is what I see if I set min 1 max 49 on the overlay > (the subjectspace.mgh file in the command) > > > > > ------------------------------------------------------------------------ > *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 2:56:38 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] problem with mri_surfcluster > When you look at the overlay in freeview and set the min thresh to 1, do > you see blobs? > > On 5/20/19 2:51 PM, Barletta, Valeria wrote: > > > > 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 > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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
