Thank you Douglas, I enjoyed reading your referral. However, I did not get answer to any of my questions. Can you take a second look?
Best, Tashrif
Date: Wed, 27 Oct 2021 11:41:35 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] orig/001.mgz to brain.mgz transformation? To: freesurfer@nmr.mgh.harvard.edu Message-ID: c72019a8-4724-f403-d309-0f5403fc21ed@mgh.harvard.edu Content-Type: text/plain; charset="utf-8" On 10/27/2021 10:58 AM, Billah, Tashrif wrote:
Hi,
- What is the name of the space of wmparc.mgz? I see that it is in the same space of brain.mgz.
Yes
What transform file brings orig/001.mgz to brain.mgz?
See https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Best, Tashrif
-------------------------------------------------------------
Tashrif Billah, MS
Research Engineer
Brigham and Women's Hospital
Harvard Medical School tbillah@bwh.harvard.edumailto:tbillah@bwh.harvard.edu
There are answers embedded in your email
On 10/27/2021 12:36 PM, Billah, Tashrif wrote:
Thank you Douglas, I enjoyed reading your referral. However, I did not get answer to any of my questions. Can you take a second look?
Best, Tashrif
Date: Wed, 27 Oct 2021 11:41:35 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] orig/001.mgz to brain.mgz transformation? To: freesurfer@nmr.mgh.harvard.edu Message-ID: c72019a8-4724-f403-d309-0f5403fc21ed@mgh.harvard.edu Content-Type: text/plain; charset="utf-8" On 10/27/2021 10:58 AM, Billah, Tashrif wrote:
Hi,
1. What is the name of the space of wmparc.mgz? I see that it is in the same space of brain.mgz.
Yes
2. What transform file brings orig/001.mgz to brain.mgz?
Seehttps://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
Best, Tashrif
*Tashrif Billah, MS*
Research Engineer
Brigham and Women's Hospital
Harvard Medical School tbillah@bwh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
1) I call the space of brain.mgz and wmparc.mgz the 'conformed' or 'native' space. As opposed to the 'anatomical' space of the raw images, and the 'standard space' (data mapped to fsaverage). I am not sure whether that's the official way though.
2) If you want the matrix, run the first command in the doc that Doug linked, but replace the '--no-save-reg' at the end with '--save-reg':
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --save-reg
You will then find the matrix in 2 formats in the directory (named 'brain-in-rawavg.mgz.lta' and 'brain-in-rawavg.mgz.reg')
Hope that helps,
Tim
On 10/27/2021 6:36 PM Billah, Tashrif tbillah@bwh.harvard.edu wrote:
Thank you Douglas, I enjoyed reading your referral. However, I did not get answer to any of my questions. Can you take a second look?
Best, Tashrif
Date: Wed, 27 Oct 2021 11:41:35 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] orig/001.mgz to brain.mgz transformation? To: freesurfer@nmr.mgh.harvard.edu Message-ID: c72019a8-4724-f403-d309-0f5403fc21ed@mgh.harvard.edu Content-Type: text/plain; charset="utf-8" On 10/27/2021 10:58 AM, Billah, Tashrif wrote:
Hi,
- What is the name of the space of wmparc.mgz? I see that it is in the same space of brain.mgz.
Yes
What transform file brings orig/001.mgz to brain.mgz?
See https://secure-web.cisco.com/1o6J13P7oCcVLae5JPqz_YrF51TlwaMLn4scuKmiZv014GE...
Best, Tashrif
Tashrif Billah, MS
Research Engineer
Brigham and Women's Hospital
Harvard Medical School tbillah@bwh.harvard.edumailto:tbillah@bwh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1mWFKxKUHzM3jPEangMpo2afop4woqPat8qZ82BY_Ah0BCC... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1R94Ly4aeMjbKGtakGbtbGCwSF388Y-BxwrHSh_4R0zI5osn... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
freesurfer@nmr.mgh.harvard.edu