This is how it looks
[cid:84da88d6-ce4d-4b97-8156-ef79f75ac6dc]
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, May 20, 2019 3:20:11 PM To: 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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
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