mri_surf2vol questions

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LGI path problem

glmfit for paired-diff on 2 groups

Govindarajan, Koushik Athreya

4 Nov 2013 4 Nov '13

9:53 a.m.

Hello Freesurfers,

I am trying to use mri_surf2vol to convert my thickness files into analyze/nifty format to use with a custom code. Is there a way I can write all output files from mri_surf2vol in axial format? Also, is there a way in FreeSurfer to combine these thickness files from both hemispheres?

Thanks in advance Koushik

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Douglas N Greve

4 Nov 4 Nov

5:46 p.m.

To get them both in one file, run mri_surf2vol to get the left hemisphere. When you run it a 2nd time for the right hemisphere add "--merge vol.lh.nii". I think FSL has software to swap dimensions doug

On 11/04/2013 09:53 AM, Govindarajan, Koushik Athreya wrote:

...

Hello Freesurfers,
       I am trying to use mri_surf2vol to convert my thickness 
files into analyze/nifty format to use with a custom code. Is there a way I can write all output files from mri_surf2vol in axial format? Also, is there a way in FreeSurfer to combine these thickness files from both hemispheres?

Thanks in advance

Koushik

Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Govindarajan, Koushik Athreya

5 Nov 5 Nov

10:48 a.m.

Many Thanks Doug. Will try that out.

Regards Koushik

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, November 04, 2013 4:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2vol questions

On 11/04/2013 09:53 AM, Govindarajan, Koushik Athreya wrote:

...

Hello Freesurfers,
       I am trying to use mri_surf2vol to convert my thickness 
files into analyze/nifty format to use with a custom code. Is there a way I can write all output files from mri_surf2vol in axial format? Also, is there a way in FreeSurfer to combine these thickness files from both hemispheres?

Thanks in advance

Koushik

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/...

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v1/url?u=https://gate.nmr.mgh.harvard.edu/... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v1/url?u=ftp://surfer.nmr.mgh.harvard.edu/... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Douglas N Greve
Govindarajan, Koushik Athreya