Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 1:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
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
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 1:29 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
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
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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.
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote:
It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
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
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote:
It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote:
Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote:
Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
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
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is this information correct?
On May 2, 2016, at 3:55 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote: It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote: Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote: Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
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
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
Douglas, can you please let me know if the voxel edit button is appropriate to use in place of the recon edit?
Thanks,
Sarah
Sent from my iPhone
On May 3, 2016, at 3:04 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
Is this information correct?
On May 2, 2016, at 3:55 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote: It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote: Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
On 5/2/16 12:14 PM, Burke,Sarah E wrote: Hello,
I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do?
Thank you
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
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sarah
no, I don't think it is. The recon edit for example will set voxels to "1" not "0" when erase so that we can keep track of them. If you are editing as part of the recon-all stream you are better off using it than just plain voxel editing.
cheers Bruce On Wed, 4 May 2016, Burke,Sarah E wrote:
Douglas, can you please let me know if the voxel edit button is appropriate to use in place of the recon edit?
Thanks,
Sarah
Sent from my iPhone
On May 3, 2016, at 3:04 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
Is this information correct?
On May 2, 2016, at 3:55 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote: It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
On 5/2/16 1:44 PM, Burke,Sarah E wrote: Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
FsTutorial/PialEdits_freeview - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview surfer.nmr.mgh.harvard.edu top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button freeview does not have a recon button. You have to run recon-all from the command line.
> On 5/2/16 12:14 PM, Burke,Sarah E wrote: > Hello, > > > I searched the mail list and saw that others have had this problem, > but I see no answers to their queries. I have version 1.0 > (5/13/2013) of Freeview for Linux. I have no recon button. What > should I do? > > > Thank you > > > > _______________________________________________ > 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
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
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 Sarah,
If you are using 5.1 you only have one button for editing, the head with the pencil in it, like you shared in your screenshot. If you click on that it will open up a box that is titled "voxel editing", but you should also see a checkbox at the top of it for "recon editing" (I attached a screenshot). If you click the checkbox you will see that the brush value gets set to 255 and the erasure value gets set to 1. This is recon editing mode and it locks in the values 255 and 1 because these are the values that FS looks for when you re-run the subject to see if the user made any changes. If you accidentally edited with different values, (say 0 instead of 1) this is where you could "run into problems down the line".
In newer versions of freeview, we have two buttons for editing (attached screenshot). One that is just for editing the aseg (which we call voxel edit), and a separate button for recon editing that looks like a head with an R in it. So in newer versions, if you want to recon edit, you just click on the head with an R and it automatically puts you in "recon mode".
Does this make sense?
You can try downloading the latest version of freeview to see what I mean. But you should be fine using the version you have, just make sure to click the checkbox for "recon editing" so that your brushes are set to the right values!
Hope this helps, Ani
On 05/04/2016 08:34 PM, Bruce Fischl wrote:
Hi Sarah
no, I don't think it is. The recon edit for example will set voxels to "1" not "0" when erase so that we can keep track of them. If you are editing as part of the recon-all stream you are better off using it than just plain voxel editing.
cheers Bruce On Wed, 4 May 2016, Burke,Sarah E wrote:
Douglas, can you please let me know if the voxel edit button is appropriate to use in place of the recon edit?
Thanks,
Sarah
Sent from my iPhone
On May 3, 2016, at 3:04 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
Is this information correct?
On May 2, 2016, at 3:55 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote: It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
On 05/02/2016 02:58 PM, Burke,Sarah E wrote:
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, May 2, 2016 2:31 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] no recon button Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.
> On 5/2/16 1:44 PM, Burke,Sarah E wrote: > Thank you Douglas. However, in the tutorial for editing output, it > says to use the recon edit button to manually perform edits. After > this step, I use the command line and recon-all. How do I do the > manual edits without this button. I do see a voxel edit button. > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview > > FsTutorial/PialEdits_freeview - Free Surfer Wiki > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview > surfer.nmr.mgh.harvard.edu > top | previous Correcting Pial Surfaces. To follow this exercise > exactly be sure you've downloaded the tutorial data set before you > begin. If you choose not to ... > > > > > ------------------------------------------------------------------------ > *From:* freesurfer-bounces@nmr.mgh.harvard.edu > freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve > greve@nmr.mgh.harvard.edu > *Sent:* Monday, May 2, 2016 1:29 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] no recon button > freeview does not have a recon button. You have to run recon-all from > the command line. > >> On 5/2/16 12:14 PM, Burke,Sarah E wrote: >> Hello, >> >> >> I searched the mail list and saw that others have had this problem, >> but I see no answers to their queries. I have version 1.0 >> (5/13/2013) of Freeview for Linux. I have no recon button. What >> should I do? >> >> >> Thank you >> >> >> >> _______________________________________________ >> 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
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes. Thank you!
Sent from my iPhone
On May 5, 2016, at 11:09 AM, Ani Varjabedian aniv@nmr.mgh.harvard.edu wrote:
Hi Sarah,
If you are using 5.1 you only have one button for editing, the head with the pencil in it, like you shared in your screenshot. If you click on that it will open up a box that is titled "voxel editing", but you should also see a checkbox at the top of it for "recon editing" (I attached a screenshot). If you click the checkbox you will see that the brush value gets set to 255 and the erasure value gets set to 1. This is recon editing mode and it locks in the values 255 and 1 because these are the values that FS looks for when you re-run the subject to see if the user made any changes. If you accidentally edited with different values, (say 0 instead of 1) this is where you could "run into problems down the line".
In newer versions of freeview, we have two buttons for editing (attached screenshot). One that is just for editing the aseg (which we call voxel edit), and a separate button for recon editing that looks like a head with an R in it. So in newer versions, if you want to recon edit, you just click on the head with an R and it automatically puts you in "recon mode".
Does this make sense?
You can try downloading the latest version of freeview to see what I mean. But you should be fine using the version you have, just make sure to click the checkbox for "recon editing" so that your brushes are set to the right values!
Hope this helps, Ani
On 05/04/2016 08:34 PM, Bruce Fischl wrote: Hi Sarah
no, I don't think it is. The recon edit for example will set voxels to "1" not "0" when erase so that we can keep track of them. If you are editing as part of the recon-all stream you are better off using it than just plain voxel editing.
cheers Bruce
On Wed, 4 May 2016, Burke,Sarah E wrote:
Douglas, can you please let me know if the voxel edit button is appropriate to use in place of the recon edit?
Thanks,
Sarah
Sent from my iPhone
On May 3, 2016, at 3:04 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
Is this information correct?
On May 2, 2016, at 3:55 PM, Burke,Sarah E saraheburke@ufl.edu wrote:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
Can you send us a link to the email you are speaking about?
On 05/02/2016 03:29 PM, Burke,Sarah E wrote: It opens a box that says "voxel edit" This allows me to edit the images accordingly, however I read in the email forum that this may create some issues further on down the line?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, May 2, 2016 3:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no recon button
what happens when you click on the button with the pencil in it? The one just above the "S" in "Surfaces"
> On 05/02/2016 02:58 PM, Burke,Sarah E wrote: > > > > ------------------------------------------------------------------------ > *From:* freesurfer-bounces@nmr.mgh.harvard.edu > freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve > greve@nmr.mgh.harvard.edu > *Sent:* Monday, May 2, 2016 2:31 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] no recon button > Can you send a snapshot of your Freeview window? The Recon Edit button > looks like a sagittal slice with an "R" in it and a pencil pointing to it. > >> On 5/2/16 1:44 PM, Burke,Sarah E wrote: >> Thank you Douglas. However, in the tutorial for editing output, it >> says to use the recon edit button to manually perform edits. After >> this step, I use the command line and recon-all. How do I do the >> manual edits without this button. I do see a voxel edit button. >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview >> >> FsTutorial/PialEdits_freeview - Free Surfer Wiki >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview >> surfer.nmr.mgh.harvard.edu >> top | previous Correcting Pial Surfaces. To follow this exercise >> exactly be sure you've downloaded the tutorial data set before you >> begin. If you choose not to ... >> >> >> >> >> ------------------------------------------------------------------------ >> *From:* freesurfer-bounces@nmr.mgh.harvard.edu >> freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve >> greve@nmr.mgh.harvard.edu >> *Sent:* Monday, May 2, 2016 1:29 PM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] no recon button >> freeview does not have a recon button. You have to run recon-all from >> the command line. >> >>> On 5/2/16 12:14 PM, Burke,Sarah E wrote: >>> Hello, >>> >>> >>> I searched the mail list and saw that others have had this problem, >>> but I see no answers to their queries. I have version 1.0 >>> (5/13/2013) of Freeview for Linux. I have no recon button. What >>> should I do? >>> >>> >>> Thank you >>> >>> >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<5.1_edits.png> <dev_edits.png> _______________________________________________ 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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Ani Varjabedian -
Bruce Fischl -
Burke,Sarah E -
Douglas Greve -
Douglas N Greve