Dear Mrs Yendiki,
thank you for your response.
However, for my configuration file, containing :
"
setenv SUBJECTS_DIR /autofs/space/avadhuti_001/users/gdesbord/CALM_data/CALM_001
set subjlist = ( 02_recon )
set dcmlist = (
/autofs/space/avadhuti_001/users/gdesbord/CALM_data/Qball_data/raw_DICOMs/CALM_001/02/892000-15-01.dcm)
set doeddy = 1
set dorotbvecs = 1
"
Did "doeddy = 1" use eddy_correct or eddy format?
Also, I am not sure about the units, is it in mm and degrees for the values in
dwi.ecclog file?
Thank you,
Sincerely,
Loic
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Tuesday, June 12, 2018 5:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dwi.ecclog file
Hi Loic - The command that computes the motion measures is dmri_motion, and it
can take either the eddy_correct or eddy format as input. The former format
contains affine registration matrices with respect to the reference frame
(which usually is the first b=0). The latter format contains the
shift/rotation/etc. parameters of the registration rather than the matrix
itself. You can run dmri_motion without arguments to see details.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daumail, Loic Jean
Sent: Tuesday, June 12, 2018 5:33:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] dwi.ecclog file
Hello,
I have several questions regarding the dwi.ecclog file data from Tracula, using
the FreeSurfer version V6.0.0.
1) Does Tracula still use eddy_correct from FSL, or was it updated with the new
eddy function from FSL?
2) Are the values for each slice of dwi.ecclog relative to the first slice or
to the previous slice, or to another template? is it the same for both rotation
and translation values?
3) What is the coordinate system for the rotation values? Is there a way to
determine the total rotation from these 9 values?
Thanks,
Sincerely,
Loic Daumail
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