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
>
>
>
>
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