Aloha fellow surfers,
I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance.
Best Sebastian
Hi Sebastian
I was able to manipulate the dialogue like this
%set gEditBrush(1,cloneSource) 1
%set gEditBrush(1,mode) 1
Try a combination of 0 or 1 for the last argument. And spaces ( or lack of them ) are absolutely important. Don't leave any space in gEditBrush(1,mode)
The first argument of gEditBrush denotes the brush. 0 means Brush 2 and 1 means Brush 3. Let us know if it works
-Krish
On Jul 28, 2010, at 3:22 PM, Sebastian Moeller wrote:
Aloha fellow surfers,
I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance.
Best Sebastian
-- Sebastian Moeller
telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Krish,
thanks a lot. Unfortunately that only sets the values for the dialog but does not actually activate them. I will try my luck, now that you showed me how to set more involved tcl structures :). I will report back (once our computer system works again).
Best Sebastian
On Jul 29, 2010, at 2:21 PM, Krish Subramaniam wrote:
Hi Sebastian
I was able to manipulate the dialogue like this
%set gEditBrush(1,cloneSource) 1
%set gEditBrush(1,mode) 1
Try a combination of 0 or 1 for the last argument. And spaces ( or lack of them ) are absolutely important. Don't leave any space in gEditBrush(1,mode)
The first argument of gEditBrush denotes the brush. 0 means Brush 2 and 1 means Brush 3. Let us know if it works
-Krish
On Jul 28, 2010, at 3:22 PM, Sebastian Moeller wrote:
Aloha fellow surfers,
I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance.
Best Sebastian
-- Sebastian Moeller
telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
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.
Hi Krish,
thanks to your pointers it was easy:
UpdateBrushInfo 0 0 5 255 1 1 (this just calls the individual "set gEditBrush($tool,field) val" in a single batch)
SetEditBrushConfiguration
and the new brush configuration is active.
best Sebastian
On Jul 29, 2010, at 2:21 PM, Krish Subramaniam wrote:
Hi Sebastian
I was able to manipulate the dialogue like this
%set gEditBrush(1,cloneSource) 1
%set gEditBrush(1,mode) 1
Try a combination of 0 or 1 for the last argument. And spaces ( or lack of them ) are absolutely important. Don't leave any space in gEditBrush(1,mode)
The first argument of gEditBrush denotes the brush. 0 means Brush 2 and 1 means Brush 3. Let us know if it works
-Krish
On Jul 28, 2010, at 3:22 PM, Sebastian Moeller wrote:
Aloha fellow surfers,
I am trying to script a few steps of my freesurfer pipeline. At the moment I am facing the problem that all my brainmasks need some manual intervention. Following advice from the wiki I try to set up tkmedit to clone from the aux to the main volume on the pressing button 3. Now my question how do I configure Button 3 from a tcl script so that my users do not have to do this manually every time? I would expect something like SetBrushInfo that takes more arguments than just brush, low, high, new, but my tcl-foo is very weak. If someone has a pointer how to set Button 3 to clone from aux vol I would be happy to hear it. Thanks in advance.
Best Sebastian
-- Sebastian Moeller
telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
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
-
Krish Subramaniam -
Sebastian Moeller