Hi Bruce,
Thanks for your reply. I was planning on doing 1. voxel based statistics with our data in SPM, and 2. Overlaying the thickness data in original subject space. But I realised I could do the same statistics using Qdec.
I had a few naive questions/clarifications about the ascii file generated for thickness, inflated and sphere surfaces. 1. The order of vertices in each of these files is the same? i.e. row 3 in thickness file should represent the same point on row 3 in the inflated and sphere files. 2. My understanding is that the coordinates are in the RAS space in each of the files? 3. The coordinates in "sphere.reg" file are in some average space? Is this MNI space? This would mean that the same coordinate in the sphere.reg files of different subjects represent the same anatomical area, right?
Best regards, Mayuresh
--- On Thu, 11/6/09, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting surface as an image volume To: "Mayuresh Korgaonkar" mayureshkorgaonkar@yahoo.co.in Cc: freesurfer@nmr.mgh.harvard.edu Date: Thursday, 11 June, 2009, 8:45 PM Hi Mayuresh,
what do you want to do with it in SPM? The thickness can be converted to a volume format, but it will actually be a 1 x n vector, where n is the # of vertices in the surface. Not sure if that will be useful or not. For example from the surf dir you could do:
mris_convert -c thickness lh.orig lh.thickness.mgz mri_convert lh.thickness.mgz lh.thickness.nii
to create a niftii file
cheers Bruce
On Thu, 11 Jun 2009, Mayuresh Korgaonkar wrote:
Dear Freesurfer users and authors,
Is it possible to export a surface (eg. ?h.thickness)
to an image volume - something which could be read into SPM?
I came across mri_surf2vol function, however I am not
to familiar with the usage. I understand that a volume registration file is required, what exactly is this file? If anyone can suggest an example usage of mri_surf2vol that will be very helpful.
Thanks in advance, Mayuresh
Explore and discover exciting
holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/
1. yes. 2. yes. 3. No, these are coordinates in our common spherical coordinate system.
cheers Bruce On Mon, 15 Jun 2009, Mayuresh Korgaonkar wrote:
Hi Bruce,
Thanks for your reply. I was planning on doing 1. voxel based statistics with our data in SPM, and 2. Overlaying the thickness data in original subject space. But I realised I could do the same statistics using Qdec.
I had a few naive questions/clarifications about the ascii file generated for thickness, inflated and sphere surfaces.
- The order of vertices in each of these files is the same? i.e. row 3 in thickness file should represent the same point on row 3 in the inflated and sphere files.
- My understanding is that the coordinates are in the RAS space in each of the files?
- The coordinates in "sphere.reg" file are in some average space? Is this MNI space? This would mean that the same coordinate in the sphere.reg files of different subjects represent the same anatomical area, right?
Best regards, Mayuresh
--- On Thu, 11/6/09, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting surface as an image volume To: "Mayuresh Korgaonkar" mayureshkorgaonkar@yahoo.co.in Cc: freesurfer@nmr.mgh.harvard.edu Date: Thursday, 11 June, 2009, 8:45 PM Hi Mayuresh,
what do you want to do with it in SPM? The thickness can be converted to a volume format, but it will actually be a 1 x n vector, where n is the # of vertices in the surface. Not sure if that will be useful or not. For example from the surf dir you could do:
mris_convert -c thickness lh.orig lh.thickness.mgz mri_convert lh.thickness.mgz lh.thickness.nii
to create a niftii file
cheers Bruce
On Thu, 11 Jun 2009, Mayuresh Korgaonkar wrote:
Dear Freesurfer users and authors,
Is it possible to export a surface (eg. ?h.thickness)
to an image volume - something which could be read into SPM?
I came across mri_surf2vol function, however I am not
to familiar with the usage. I understand that a volume registration file is required, what exactly is this file? If anyone can suggest an example usage of mri_surf2vol that will be very helpful.
Thanks in advance, Mayuresh
Explore and discover exciting
holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Mayuresh Korgaonkar