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
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
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
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
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
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
This is what I see if I set min 1 max 49 on the overlay (the subjectspace.mgh file in the command)
[cid:219fb126-a40e-4f06-9849-aac62b6aee0f]
________________________________ 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
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
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
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
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
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
Please not that I chose a new mask because the other wasn't well visible. This is in the right hemisphere, I obtained the same type of error (0 vertices found)
[cid:2e6b5919-00b7-4a25-a6db-688ce3a989a3]
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Barletta, Valeria VBARLETTA@mgh.harvard.edu Sent: Tuesday, May 21, 2019 10:23:39 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with mri_surfcluster
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
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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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
[cid:part1.08657764.3E97CB01@mgh.harvard.edu]
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Monday, May 20, 2019 3:20:11 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Monday, May 20, 2019 2:56:38 PM *To:* freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Monday, May 20, 2019 2:46:54 PM *To:* freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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
[cid:part1.08657764.3E97CB01@mgh.harvard.edu]
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Monday, May 20, 2019 3:20:11 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Monday, May 20, 2019 2:56:38 PM *To:* freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu *Sent:* Monday, May 20, 2019 2:46:54 PM *To:* freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@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-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas
N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@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-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas
N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@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
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freesurfer@nmr.mgh.harvard.edu
-
Barletta, Valeria -
Greve, Douglas N.,Ph.D.