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,

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?

See https://secure-web.cisco.com/1o6J13P7oCcVLae5JPqz_YrF51TlwaMLn4scuKmiZv014GE...

...

Best, Tashrif

---

Tashrif Billah, MS

Research Engineer

Brigham and Women's Hospital

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