yes, I often use voxel and vertex interchangeably On 5/21/19 10:58 AM, Barletta, Valeria wrote: > I see, that makes sense. > But why are you mentioning voxels? Shouldn't they be vertices since my > mask is registered to the surface? (I used vol2surf to do it) > ------------------------------------------------------------------------ > *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:* Tuesday, May 21, 2019 10:31:57 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] problem with mri_surfcluster > it looks like there are only a few voxels in your mask. If they do not > match up with the superthreshold voxels in the map, then you will not > have any voxels to make a cluster with > > On 5/21/2019 10:23 AM, Barletta, Valeria wrote: >> >> This is how it looks >> >> >> >> ------------------------------------------------------------------------ >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu> >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, >> Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu> >> *Sent:* Monday, May 20, 2019 3:20:11 PM >> *To:* freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] problem with mri_surfcluster >> 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 >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> > <freesurfer-boun...@nmr.mgh.harvard.edu> >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, >> Douglas >> > N.,Ph.D. <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu> >> > *Sent:* Monday, May 20, 2019 2:56:38 PM >> > *To:* freesurfer@nmr.mgh.harvard.edu >> <mailto: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 >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> > > <freesurfer-boun...@nmr.mgh.harvard.edu> >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, >> Douglas >> > > N.,Ph.D. <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu> >> > > *Sent:* Monday, May 20, 2019 2:46:54 PM >> > > *To:* freesurfer@nmr.mgh.harvard.edu >> <mailto: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 >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > >> > > _______________________________________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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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