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 <sarahebu...@ufl.edu> wrote:
Is this information correct?
On May 2, 2016, at 3:55 PM, Burke,Sarah E <sarahebu...@ufl.edu> wrote:
https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg38934.html
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N Greve <gr...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N Greve <gr...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve
<gr...@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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
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Freesurfer mailing list
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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
gr...@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
_______________________________________________
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.
