Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edumailto:Vy_dinh@rush.edu
I don't know about the rest, but you can change the cursor and surface colors with View->Configure
Vy Dinh wrote:
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu mailto:Vy_dinh@rush.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks!
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, October 13, 2011 1:25 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Automatic corrections log/diary and questions about Tkmedit color options
I don't know about the rest, but you can change the cursor and surface colors with View->Configure
Vy Dinh wrote:
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu mailto:Vy_dinh@rush.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
I believe if you go to the View menu you can select "Edited voxels" which will show what you edited in that session in blue.
If you run: recon-all -show-edits -s subjid
this will show you white matter and brainmask edits you have made I belive.
We don't print a log of the manual correections but that is an interesting idea. Allison
On Thu, 13 Oct 2011, Douglas N Greve wrote:
I don't know about the rest, but you can change the cursor and surface colors with View->Configure
Vy Dinh wrote:
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu mailto:Vy_dinh@rush.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is very neat. Thank you everyone for your responses!
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
________________________________________ From: Allison Player [astevens@nmr.mgh.harvard.edu] Sent: Thursday, October 13, 2011 2:10 PM To: Douglas N Greve Cc: Vy Dinh; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Automatic corrections log/diary and questions about Tkmedit color options
I believe if you go to the View menu you can select "Edited voxels" which will show what you edited in that session in blue.
If you run: recon-all -show-edits -s subjid
this will show you white matter and brainmask edits you have made I belive.
We don't print a log of the manual correections but that is an interesting idea. Allison
On Thu, 13 Oct 2011, Douglas N Greve wrote:
I don't know about the rest, but you can change the cursor and surface colors with View->Configure
Vy Dinh wrote:
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu mailto:Vy_dinh@rush.edu
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.
we do however record manual edits in the volumes themselves. Erasing sets things to 1 (not 0) and editing them on turns them to 255 so you can always recover edits that you have made
cheers Bruce On Thu, 13 Oct 2011, Allison Player wrote:
I believe if you go to the View menu you can select "Edited voxels" which will show what you edited in that session in blue.
If you run: recon-all -show-edits -s subjid
this will show you white matter and brainmask edits you have made I belive.
We don't print a log of the manual correections but that is an interesting idea. Allison
On Thu, 13 Oct 2011, Douglas N Greve wrote:
I don't know about the rest, but you can change the cursor and surface colors with View->Configure
Vy Dinh wrote:
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu mailto:Vy_dinh@rush.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
From your last response, does that mean then that we can add the voxels back to extend the pial surface that we mistakenly retracted in the previous edit?
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, October 13, 2011 3:13 PM To: Allison Player Cc: Douglas N Greve; Vy Dinh; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Automatic corrections log/diary and questions about Tkmedit color options
we do however record manual edits in the volumes themselves. Erasing sets things to 1 (not 0) and editing them on turns them to 255 so you can always recover edits that you have made
cheers Bruce On Thu, 13 Oct 2011, Allison Player wrote:
I believe if you go to the View menu you can select "Edited voxels" which will show what you edited in that session in blue.
If you run: recon-all -show-edits -s subjid
this will show you white matter and brainmask edits you have made I belive.
We don't print a log of the manual correections but that is an interesting idea. Allison
On Thu, 13 Oct 2011, Douglas N Greve wrote:
I don't know about the rest, but you can change the cursor and surface colors with View->Configure
Vy Dinh wrote:
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu mailto:Vy_dinh@rush.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
sure On Fri, 14 Oct 2011, Vy Dinh wrote:
Hi Bruce,
From your last response, does that mean then that we can add the voxels back to extend the pial surface that we mistakenly retracted in the previous edit?
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Thursday, October 13, 2011 3:13 PM To: Allison Player Cc: Douglas N Greve; Vy Dinh; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Automatic corrections log/diary and questions about Tkmedit color options
we do however record manual edits in the volumes themselves. Erasing sets things to 1 (not 0) and editing them on turns them to 255 so you can always recover edits that you have made
cheers Bruce On Thu, 13 Oct 2011, Allison Player wrote:
I believe if you go to the View menu you can select "Edited voxels" which will show what you edited in that session in blue.
If you run: recon-all -show-edits -s subjid
this will show you white matter and brainmask edits you have made I belive.
We don't print a log of the manual correections but that is an interesting idea. Allison
On Thu, 13 Oct 2011, Douglas N Greve wrote:
I don't know about the rest, but you can change the cursor and surface colors with View->Configure
Vy Dinh wrote:
Dear Experts,
Does Freesurfer print an automatic log or diary of the manual corrections (to a brainmask) made in Tkmedit?
Also, is there any way that I can change the color of the edited voxels? It would be great to view the edited voxels as anything but black and white (eg dark blue and a bright yellow respectively) when reviewing the corrections. Is it possible to change the color of the crosshair or the surface boundaries? Because the crosshair and the pial surface boundary are both red, it is quite difficult to locate the crosshair when changing the views. I am also concerned that the red/green lines may be an issue for colorblind users.
Best,
Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh@rush.edu mailto:Vy_dinh@rush.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@nmr.mgh.harvard.edu
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Allison Player -
Bruce Fischl -
Douglas N Greve -
Vy Dinh