Re: [Freesurfer] dwi.ecclog file
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
[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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.