Hi,
I can extract subcorical objects from freesurfer segmentation, since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.
Thanks Shahab
--------------------------------- Get your email and more, right on the new Yahoo.com
Hi Shahab,
the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them?
cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:
Hi,
I can extract subcorical objects from freesurfer segmentation, since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.
Thanks Shahab
Get your email and more, right on the new Yahoo.com
Hi,
I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in the reply. My final goal is to have Cortical Regions segmented at the subjects native coordinate space. And I prefer to have the segmentation in analyze format.
and also, I was wondering if 1- there is a way of saving Surfaces generated with FreeSurfer into an analyze image. 2- If we can control how fine the cortical segmentation be. (the number of regions segmented).
Behrang,
On 9/23/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shahab,
the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them?
cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:
Hi,
I can extract subcorical objects from freesurfer segmentation, since
each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.
Thanks Shahab
Get your email and more, right on the new Yahoo.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, sorry, analyze is a volume format and doesn't support surface representations. And we support 2 different parcellation types, but they are fixed in terms of what they represent.
Bruce On Sat, 23 Sep 2006, Behrang Nosrat Makouei wrote:
Hi,
I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in the reply. My final goal is to have Cortical Regions segmented at the subjects native coordinate space. And I prefer to have the segmentation in analyze format.
and also, I was wondering if 1- there is a way of saving Surfaces generated with FreeSurfer into an analyze image. 2- If we can control how fine the cortical segmentation be. (the number of regions segmented).
Behrang,
On 9/23/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shahab,
the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them?
cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:
Hi,
I can extract subcorical objects from freesurfer segmentation, since
each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.
Thanks Shahab
Get your email and more, right on the new Yahoo.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Have you looked at the aparc+aseg.mgz? It has cortical and subcortical labelings. You can convert it to analyze with mri_convert.
Behrang Nosrat Makouei wrote:
Hi,
I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in the reply. My final goal is to have Cortical Regions segmented at the subjects native coordinate space. And I prefer to have the segmentation in analyze format.
and also, I was wondering if 1- there is a way of saving Surfaces generated with FreeSurfer into an analyze image. 2- If we can control how fine the cortical segmentation be. (the number of regions segmented).
Behrang,
On 9/23/06, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Shahab, the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them? cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote: > Hi, > > I can extract subcorical objects from freesurfer segmentation, since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer. > > Thanks > Shahab > > > --------------------------------- > Get your email and more, right on the new Yahoo.com <http://Yahoo.com> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>-- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, thanks for help. That was the segmentation i was looking for. Now the question is what is the look up table Freesurfer uses to assign values to different labels? in other words, if I want to segment the "G_postcentral" (for e.g.) what value should i look for? bets
On 9/25/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Have you looked at the aparc+aseg.mgz? It has cortical and subcortical labelings. You can convert it to analyze with mri_convert.
Behrang Nosrat Makouei wrote:
Hi,
I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in the reply. My final goal is to have Cortical Regions segmented at the subjects native coordinate space. And I prefer to have the segmentation in analyze format.
and also, I was wondering if 1- there is a way of saving Surfaces generated with FreeSurfer into an analyze image. 2- If we can control how fine the cortical segmentation be. (the number of regions segmented).
Behrang,
On 9/23/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shahab,
the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them?
cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:
Hi,
I can extract subcorical objects from freesurfer segmentation, since
each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.
Thanks Shahab
Get your email and more, right on the new Yahoo.comhttp://yahoo.com/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Look in $FREESURFER_HOME/FreeSurferColorLUT.txt
Behrang Nosrat Makouei wrote:
Hi, thanks for help. That was the segmentation i was looking for. Now the question is what is the look up table Freesurfer uses to assign values to different labels? in other words, if I want to segment the " G_postcentral" (for e.g.) what value should i look for? bets
On 9/25/06, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Have you looked at the aparc+aseg.mgz? It has cortical and subcortical labelings. You can convert it to analyze with mri_convert. Behrang Nosrat Makouei wrote:Hi, I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in the reply. My final goal is to have Cortical Regions segmented at the subjects native coordinate space. And I prefer to have the segmentation in analyze format. and also, I was wondering if 1- there is a way of saving Surfaces generated with FreeSurfer into an analyze image. 2- If we can control how fine the cortical segmentation be. (the number of regions segmented). Behrang, On 9/23/06, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Shahab, the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them? cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:Hi,
I can extract subcorical objects from freesurfer
segmentation, since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.Thanks Shahab
Get your email and more, right on the new Yahoo.com
<http://yahoo.com/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
Hi again, I am trying to convert a surface segmentation into a volume file, here is the command I am using:
mri_surf2vol --surfval (???) --hemi lh --surf orig --volregidentity c2 --template ../mri/rawavg.mgz --outvol orig.img
now my question is what should go to surface value argument. My understanding from freesurfer surface files was that they store some kind of values for each vertex too, so when loading a color table, it simply assigns a color to the vertex values and labels them. So if surface files already have the surface values, what is this field actually refers too? I hope my question is clear enough.
best
On 9/25/06, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Look in $FREESURFER_HOME/FreeSurferColorLUT.txt
Behrang Nosrat Makouei wrote:
Hi, thanks for help. That was the segmentation i was looking for. Now the question is what is the look up table Freesurfer uses to assign values to different labels? in other words, if I want to segment the "G_postcentral" (for e.g.) what value should i look for? bets
On 9/25/06, Doug Greve <greve@nmr.mgh.harvard.edu > wrote:
Have you looked at the aparc+aseg.mgz? It has cortical and subcortical labelings. You can convert it to analyze with mri_convert.
Behrang Nosrat Makouei wrote:
Hi,
I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in the reply. My final goal is to have Cortical Regions segmented at the subjects native coordinate space. And I prefer to have the segmentation in analyze format.
and also, I was wondering if 1- there is a way of saving Surfaces generated with FreeSurfer into an analyze image. 2- If we can control how fine the cortical segmentation be. (the number of regions segmented).
Behrang,
On 9/23/06, Bruce Fischl <fischl@nmr.mgh.harvard.edu > wrote:
Hi Shahab,
the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them?
cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:
Hi,
I can extract subcorical objects from freesurfer segmentation,
since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.
Thanks Shahab
Get your email and more, right on the new Yahoo.comhttp://yahoo.com/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Use mri_label2vol, not mri_surf2vol.
doug
Behrang Nosrat Makouei wrote:
Hi again, I am trying to convert a surface segmentation into a volume file, here is the command I am using:
mri_surf2vol --surfval (???) --hemi lh --surf orig --volregidentity c2 --template ../mri/rawavg.mgz --outvol orig.img
now my question is what should go to surface value argument. My understanding from freesurfer surface files was that they store some kind of values for each vertex too, so when loading a color table, it simply assigns a color to the vertex values and labels them. So if surface files already have the surface values, what is this field actually refers too? I hope my question is clear enough.
best
On 9/25/06, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Look in $FREESURFER_HOME/FreeSurferColorLUT.txt Behrang Nosrat Makouei wrote:Hi, thanks for help. That was the segmentation i was looking for. Now the question is what is the look up table Freesurfer uses to assign values to different labels? in other words, if I want to segment the " G_postcentral" (for e.g.) what value should i look for? bets On 9/25/06, Doug Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Have you looked at the aparc+aseg.mgz? It has cortical and subcortical labelings. You can convert it to analyze with mri_convert. Behrang Nosrat Makouei wrote:Hi, I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in the reply. My final goal is to have Cortical Regions segmented at the subjects native coordinate space. And I prefer to have the segmentation in analyze format. and also, I was wondering if 1- there is a way of saving Surfaces generated with FreeSurfer into an analyze image. 2- If we can control how fine the cortical segmentation be. (the number of regions segmented). Behrang, On 9/23/06, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Shahab, the ?h.*.annot files are the cortical labelings. What exactly do you wat to do with them? cheers, Bruce On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:Hi,
I can extract subcorical objects from freesurfer
segmentation, since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer.Thanks Shahab
Get your email and more, right on the new Yahoo.com
<http://yahoo.com/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Behrang Nosrat Makouei, Engineering Science, MICA Lab (MIAL), TASC 9400, SFU. cell: 778-885-5016
freesurfer@nmr.mgh.harvard.edu
-
Behrang Nosrat Makouei -
Bruce Fischl -
Doug Greve -
Shahabuddin Ansari