Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot! Guang _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2...
you can load it in tkmedit from the file menu and probe it one voxel at a time, or you can use
mri_convert atlas.gca#0 means.mgz
and
mri_convert atlas.gca#1 priors.mgz labels.mgz
to look at the most likely label and it's mean
cheers, Bruce
On Thu, 29 Oct 2009, Guang Zeng wrote:
Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot! Guang
New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2...
Hello, Bruce,
Thanks for your reply. I still have two questions,
1. Does these gca files also include 9 arrays such as those template files saved into .tiff file. Is there any place in the WIKI explain the format of the gca files?
What is the difference between gca#0 and gca#1?
2. I tried the command line you suggested,
mri_convert atlas.gca#1 priors.mgz labels.mgz
It gave me an error message:
mri_convert: extra argument ("labels.mgz")
type mri_convert -u for usage
Thanks a lot! Guang
Date: Thu, 29 Oct 2009 07:21:42 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
you can load it in tkmedit from the file menu and probe it one voxel at a time, or you can use
mri_convert atlas.gca#0 means.mgz
and
mri_convert atlas.gca#1 priors.mgz labels.mgz
to look at the most likely label and it's mean
cheers, Bruce
On Thu, 29 Oct 2009, Guang Zeng wrote:
Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot! Guang
New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/
Hi Guang,
it should be:
mri_convert atlas.gca#0 means.mgz mri_convert atlas.gca#1 labels.mgz mri_convert atlas.gca#2 priors.mgz
cheers, Bruce
p.s. sorry, I don't think the gca format is documented anywhere, but you are welcome to the code if you want
On Thu, 28 Jan 2010, Guang Zeng wrote:
Hello, Bruce,
Thanks for your reply. I still have two questions,
- Does these gca files also include 9 arrays such as those template files saved into .tiff file.
Is there any place in the WIKI explain the format of the gca files?
What is the difference between gca#0 and gca#1?
- I tried the command line you suggested,
mri_convert atlas.gca#1 priors.mgz labels.mgz
It gave me an error message:
mri_convert: extra argument ("labels.mgz")
type mri_convert -u for usage
Thanks a lot! Guang
Date: Thu, 29 Oct 2009 07:21:42 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
you can load it in tkmedit from the file menu and probe it one voxel at a time, or you can use
mri_convert atlas.gca#0 means.mgz
and
mri_convert atlas.gca#1 priors.mgz labels.mgz
to look at the most likely label and it's mean
cheers, Bruce
On Thu, 29 Oct 2009, Guang Zeng wrote:
Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot! Guang
New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hotmail: Trusted email with Microsoft?s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/
Hello, Bruce,
Thanks a lot for your quick reply? Could I ask what is the difference between labels.mgz and priors.mgz (or atlas.gca#1 and atlas.gca#2). I load both of them in tkmedit, move the mouse in the image, they all gave me the same value.
Thanks! Guang
Date: Thu, 28 Jan 2010 16:51:56 -0500 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] how to view .gca file
Hi Guang,
it should be:
mri_convert atlas.gca#0 means.mgz mri_convert atlas.gca#1 labels.mgz mri_convert atlas.gca#2 priors.mgz
cheers, Bruce
p.s. sorry, I don't think the gca format is documented anywhere, but you are welcome to the code if you want
On Thu, 28 Jan 2010, Guang Zeng wrote:
Hello, Bruce,
Thanks for your reply. I still have two questions,
- Does these gca files also include 9 arrays such as those template files saved into .tiff file.
Is there any place in the WIKI explain the format of the gca files?
What is the difference between gca#0 and gca#1?
- I tried the command line you suggested,
mri_convert atlas.gca#1 priors.mgz labels.mgz
It gave me an error message:
mri_convert: extra argument ("labels.mgz")
type mri_convert -u for usage
Thanks a lot! Guang
Date: Thu, 29 Oct 2009 07:21:42 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
you can load it in tkmedit from the file menu and probe it one voxel at a time, or you can use
mri_convert atlas.gca#0 means.mgz
and
mri_convert atlas.gca#1 priors.mgz labels.mgz
to look at the most likely label and it's mean
cheers, Bruce
On Thu, 29 Oct 2009, Guang Zeng wrote:
Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot! Guang
New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hotmail: Trusted email with Microsoft?s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/
_________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/
really? Hmmm, that sounds like a bug. It should be:
labels --> indices of the most likely label at each voxel priors --> the probability that that label occurs at that voxel means --> the mean intensity of the most likely label
you can also use -nth $frame instead of #$frame
On Thu, 28 Jan 2010, Guang Zeng wrote:
Hello, Bruce,
Thanks a lot for your quick reply? Could I ask what is the difference between labels.mgz and priors.mgz (or atlas.gca#1 and atlas.gca#2). I load both of them in tkmedit, move the mouse in the image, they all gave me the same value.
Thanks! Guang
Date: Thu, 28 Jan 2010 16:51:56 -0500 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] how to view .gca file
Hi Guang,
it should be:
mri_convert atlas.gca#0 means.mgz mri_convert atlas.gca#1 labels.mgz mri_convert atlas.gca#2 priors.mgz
cheers, Bruce
p.s. sorry, I don't think the gca format is documented anywhere, but you are welcome to the code if you want
On Thu, 28 Jan 2010, Guang Zeng wrote:
Hello, Bruce,
Thanks for your reply. I still have two questions,
- Does these gca files also include 9 arrays such as those template files saved into .tiff file.
Is there any place in the WIKI explain the format of the gca files?
What is the difference between gca#0 and gca#1?
- I tried the command line you suggested,
mri_convert atlas.gca#1 priors.mgz labels.mgz
It gave me an error message:
mri_convert: extra argument ("labels.mgz")
type mri_convert -u for usage
Thanks a lot! Guang
Date: Thu, 29 Oct 2009 07:21:42 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
you can load it in tkmedit from the file menu and probe it one voxel at a time, or you can use
mri_convert atlas.gca#0 means.mgz
and
mri_convert atlas.gca#1 priors.mgz labels.mgz
to look at the most likely label and it's mean
cheers, Bruce
On Thu, 29 Oct 2009, Guang Zeng wrote:
Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot! Guang
New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hotmail: Trusted email with Microsoft?s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/
Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/
there's a wiki page with a bit of info, including the gca.c/h files:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat
On Thu, 2010-01-28 at 17:09 -0500, Bruce Fischl wrote:
really? Hmmm, that sounds like a bug. It should be:
labels --> indices of the most likely label at each voxel priors --> the probability that that label occurs at that voxel means --> the mean intensity of the most likely label
you can also use -nth $frame instead of #$frame
On Thu, 28 Jan 2010, Guang Zeng wrote:
Hello, Bruce,
Thanks a lot for your quick reply? Could I ask what is the difference between labels.mgz and priors.mgz (or atlas.gca#1 and atlas.gca#2). I load both of them in tkmedit, move the mouse in the image, they all gave me the same value.
Thanks! Guang
Date: Thu, 28 Jan 2010 16:51:56 -0500 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] how to view .gca file
Hi Guang,
it should be:
mri_convert atlas.gca#0 means.mgz mri_convert atlas.gca#1 labels.mgz mri_convert atlas.gca#2 priors.mgz
cheers, Bruce
p.s. sorry, I don't think the gca format is documented anywhere, but you are welcome to the code if you want
On Thu, 28 Jan 2010, Guang Zeng wrote:
Hello, Bruce,
Thanks for your reply. I still have two questions,
- Does these gca files also include 9 arrays such as those template files saved into .tiff file.
Is there any place in the WIKI explain the format of the gca files?
What is the difference between gca#0 and gca#1?
- I tried the command line you suggested,
mri_convert atlas.gca#1 priors.mgz labels.mgz
It gave me an error message:
mri_convert: extra argument ("labels.mgz")
type mri_convert -u for usage
Thanks a lot! Guang
Date: Thu, 29 Oct 2009 07:21:42 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
you can load it in tkmedit from the file menu and probe it one voxel at a time, or you can use
mri_convert atlas.gca#0 means.mgz
and
mri_convert atlas.gca#1 priors.mgz labels.mgz
to look at the most likely label and it's mean
cheers, Bruce
On Thu, 29 Oct 2009, Guang Zeng wrote:
Hi, there,
I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab?
Is it possible to replace FS Atlas with our own Atlas and use it for analysis?
Thanks a lot! Guang
New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hotmail: Trusted email with Microsoft?s powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390706/direct/01/
Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Guang Zeng -
Nick Schmansky