Re: [Freesurfer] questions about Tracula and doeddy=1 or 0
Dear FreeSurfer experts, I had sent several times this email since the last few months, and never obtained any reply. Would anyone be able to provide me little bit of insight please? I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0. b1=0, b2=3000 s/mm2 and diff directions = 90. Surprisingly the trac-all reconstruction with doeddy =1 was not as good as with doeddy = 0 on average on all the subjects, as in our dataset there were more tracts missing with doeddy=1 among all the subjects, which is a very curious result, shouldn't we get the reverse? ==> should I rely more on the doeddy=0 result then? ==> or should I modify the configuration parameters, such as adding more control points , ... and maybe others? Secondly, we are using the head motion parameters (computed with doeddy=1) to exclude subjects who moved too much. Is that appropriate? In other words, can we trust the motion parameters and exclude subjects on that basis? Thank you for your time and consideration, Sincerely, Loïc Daumail Graduate Intern at Athinoula A. Martinos Center for Biomedical Imaging MGH/HST From: Daumail, Loic Jean Sent: Thursday, July 12, 2018 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Cc: gdesb...@nmr.mgh.harvard.edu Subject: questions about Tracula and doeddy=1 or 0 Dear FreeSurfer experts, I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0. b1=0, b2=3000 s/mm2 and diff directions = 90. Surprisingly the trac-all reconstruction with doeddy =1 was not as good as with doeddy = 0 on average on all the subjects, as in our dataset there were more tracts missing with doeddy=1 among all the subjects, which is a very curious result, shouldn't we get the reverse? ==> should I rely more on the doeddy=0 result then? ==> or should I modify the configuration parameters, such as adding more control points , ... and maybe others? Secondly, we are using the head motion parameters (computed with doeddy=1) to exclude subjects who moved too much. Is that appropriate? In other words, can we trust the motion parameters and exclude subjects on that basis? Thank you for your time and consideration, Sincerely, Loic ___ 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] Question about Freeview, 20% threshold
Dear FreeSurfer experts, I am currently using TRACULA( from freeSurfer 6.0), and on the freeview visualization of merged files of the probability distributions of the tracts, I don't understand the thing about the "20% threshold". Indeed, on the tracula tutorial, it is written that the tracts are displayed in a way that they are at 20% of their maximum threshold. However, what does this mean? Is it the 20% of the most probable paths for each tracts? The adjustment bar on the side of the screen permits to vary this threshold, but when we reduce the level of the threshold, the size of the tracts increase, which seems in contradiction with the previous statements... I then suppose that my guess must be wrong? Thank you for your time and consideration! Sincerely, Loïc ___ 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] questions about Tracula and doeddy=1 or 0
Dear FreeSurfer experts, I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0. b1=0, b2=3000 s/mm2 and diff directions = 90. Surprisingly the trac-all reconstruction with doeddy =1 was not as good as with doeddy = 0 on average on all the subjects, as in our dataset there were more tracts missing with doeddy=1 among all the subjects, which is a very curious result, shouldn't we get the reverse? ==> should I rely more on the doeddy=0 result then? ==> or should I modify the configuration parameters, such as adding more control points , ... and maybe others? Secondly, we are using the head motion parameters (computed with doeddy=1) to exclude subjects who moved too much. Is that appropriate? In other words, can we trust the motion parameters and exclude subjects on that basis? Thank you for your time and consideration, Sincerely, Loic ___ 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] [TRACULA] eddy_correct /affine registration matrices / motion/ eddy currents
Dear FreeSurfer experts, I would like to understand better the principle of eddy_correct: -in which way the eddy currents caused by motion are set apart from the eddy currents caused by fast switching diffusion-encoding gradients? -and then, how are the affine registration matrices reflecting motion computed by eddy_correct considering the previous issues? -does eddy_correct even computes these affine registration matrices(dwi.ecclog)? or is it another tool of dmri_motion? Thanks, Loïc Daumail Graduate intern at Athinoula A. Martinos Center for Biomedical Imaging MGH/HST ___ 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
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.
[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.
