I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key.
By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....*
However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas?
Jared
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5
Kernel info: Darwin 8.9.1 i386
---------------------------------------------------------------------
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT?
On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote:
I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key.
By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....*
However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas?
Jared
Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say "target layer."
Kevin Teich wrote:
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT?
On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote:
I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key.
By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....*
However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas?
Jared
Sorry, I was thinking you were talking about Scuba.
Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window?
If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters.
Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog?
On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote:
Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say "target layer."
Kevin Teich wrote:
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT?
On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote:
I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key.
By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....*
However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas?
In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool.
Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the "Sgmtn label" (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the "Sgmtn label" line says "Right-accumbens-intens" and the paint is grey or white depending on the background color of the segmentation label map.
Any further ideas? Thanks.
Kevin Teich wrote:
Sorry, I was thinking you were talking about Scuba.
Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window?
If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters.
Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog?
On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote:
Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say "target layer."
Kevin Teich wrote:
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT?
On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote:
I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key.
By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....*
However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas?
Hi Jared,
How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the "Sgmtn label" (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the "Sgmtn label" line says "Right-accumbens-intens" and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks.
Kevin Teich wrote:
Sorry, I was thinking you were talking about Scuba.
Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window?
If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters.
Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog?
On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote:
Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say "target layer."
Kevin Teich wrote:
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT?
On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote:
I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key.
By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Jenni Pacheco wrote:
Hi Jared,
How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the "Sgmtn label" (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the "Sgmtn label" line says "Right-accumbens-intens" and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks.
Kevin Teich wrote:
Sorry, I was thinking you were talking about Scuba.
Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window?
If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters.
Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog?
On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote:
Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say "target layer."
Kevin Teich wrote:
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT?
On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote:
I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key.
By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the "Sgmnt label" when I attempt to edit the segmentation.
When you are editing the segmentation, are you using the middle button to change the label?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
Jenni Pacheco wrote:
Hi Jared,
How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the "Sgmtn label" (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the "Sgmtn label" line says "Right-accumbens-intens" and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks.
Kevin Teich wrote:
Sorry, I was thinking you were talking about Scuba.
Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window?
If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters.
Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog?
On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote:
Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say "target layer."
Kevin Teich wrote:
Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT?
On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote:
> I am attempting to edit the segmentation results in TkMedit, according > to the following Wiki directions ( > > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): > A segmentation can be edited with the Edit Segmentation tool, which > can be activated by pushing the icon_copy.gif button on the Main > Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the > 'g' key. > > By clicking with button 2 with this tool, you can 'paint' a label in > the segmentation. The color used can be set in the dialog box brought > up by choosing *Tools->Configure Segmentation Brush....* However, I am > not able to change the color to match the structure I am wanting to > edit (I have tried selecting three different structures at random and > the color of the editing remains grey). Any ideas? >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the "Sgmnt label" when I attempt to edit the segmentation.
Jenni Pacheco wrote:
When you are editing the segmentation, are you using the middle button to change the label?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
Jenni Pacheco wrote:
Hi Jared,
How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the "Sgmtn label" (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the "Sgmtn label" line says "Right-accumbens-intens" and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks.
Kevin Teich wrote:
Sorry, I was thinking you were talking about Scuba.
Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window?
If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters.
Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog?
On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote:
Yes, I believe so. The layer's color map is set to FreeSurferColorLUT.txt when loading the segmentation. The Segmentation Brush source is set at Segmentation (under Configure Segmentation Brush)--I imagine that's what you are referring to when you say "target layer."
Kevin Teich wrote:
> Are you sure the Target Layer is set to the segmentation volume > layer? And that that layer's color map type is set to LUT? > > On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: > >> I am attempting to edit the segmentation results in TkMedit, >> according to the following Wiki directions ( > >> TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): >> A segmentation can be edited with the Edit Segmentation tool, >> which can be activated by pushing the icon_copy.gif button on >> the Main Toolbar, by choosing *Tools->Edit Segmentation*, or by >> pressing the 'g' key. >> >> By clicking with button 2 with this tool, you can 'paint' a >> label in the segmentation. The color used can be set in the >> dialog box brought up by choosing *Tools->Configure >> Segmentation Brush....* However, I am not able to change the >> color to match the structure I am wanting to edit (I have tried >> selecting three different structures at random and the color of >> the editing remains grey). Any ideas? >>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the "Sgmnt label" when I attempt to edit the segmentation.
Jenni,
Thanks--it was a button issue. It is working now!
I was confused because I was following the Wiki directions (http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditWorkingWithDa...) and on my Mac, it is Button 3 (according to System Preferences) that paints a label in the segmentation, not Button 2 as indicated. I didn't know what you meant by the "middle button", but I started to experiment and discovered it was Button 3 that paints the label. Thanks again for your help.
Should I change this Wiki page to indicate that it is Button 3 or is this just an issue for those who use Macs with the new standard Mac mouse?
Best,
Jared
It's a MAC thing. With a standard three-button mouse it's the middle button that adds the label. If you use a MAC mouse or other non 3-button mouse there are other keystrokes which you may have to do in order to have the middle button option.
sorry, Jenni
On Fri, 18 May 2007, Jared Conley wrote:
Jenni Pacheco wrote:
When you are editing the segmentation, are you using the middle button to change the label?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
Jenni Pacheco wrote:
Hi Jared,
How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there?
jenni
On Fri, 18 May 2007, Jared Conley wrote:
In response to the questions, I do see the segmentation properly in colors (as a translucent color overlay on the anatomical), and I am sure I am using the Edit Segmentation tool. Clicking and dragging with the tool does change the segmentation volume, it just does not change it to the "Sgmtn label" (in the tools window) that I want. It doesn't matter what value I choose in the Segmentation Brush Info, the "Sgmtn label" line says "Right-accumbens-intens" and the paint is grey or white depending on the background color of the segmentation label map. Any further ideas? Thanks.
Kevin Teich wrote:
Sorry, I was thinking you were talking about Scuba.
Do you see the segmentation properly, in colors? If not, there was probably an error in loading the segmentation; do you see any errors in the shell window?
If you do see the segmentation volume displayed properly as a translucent color overlay on the anatomical, are you sure you are using the Edit Segmentation tool? It's a paintbrush over a volume divided into quarters.
Does clicking and dragging with the tool actually change the segmentation volume, that is, can you mouse over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog?
On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote:
> Yes, I believe so. The layer's color map is set to > FreeSurferColorLUT.txt when loading the segmentation. The > Segmentation Brush source is set at Segmentation (under Configure > Segmentation Brush)--I imagine that's what you are referring to when > you say "target layer." > > Kevin Teich wrote: > >> Are you sure the Target Layer is set to the segmentation volume >> layer? And that that layer's color map type is set to LUT? >> >> On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: >> >>> I am attempting to edit the segmentation results in TkMedit, >>> according to the following Wiki directions ( > >>> TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): >>> A segmentation can be edited with the Edit Segmentation tool, which >>> can be activated by pushing the icon_copy.gif button on the Main >>> Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the >>> 'g' key. >>> >>> By clicking with button 2 with this tool, you can 'paint' a label in >>> the segmentation. The color used can be set in the dialog box >>> brought up by choosing *Tools->Configure Segmentation Brush....* >>> However, I am not able to change the color to match the structure I >>> am wanting to edit (I have tried selecting three different >>> structures at random and the color of the editing remains grey). >>> Any ideas? >>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Jenni for the assistance. Yes, I have gone to Tools/Configure Segmentation Brush.../Segmentation Brush Info in the TkMedit Tools window. In the Segmentation Brush Info window, I have selected my desired structure color (with the Main Anatomical used as source) and still no change in the "Sgmnt label" when I attempt to edit the segmentation.
Jenni,
Thanks--it was a button issue. It is working now! I was confused because I was following the Wiki directions (http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditWorkingWithDa...) and on my Mac, it is Button 3 (according to System Preferences) that paints a label in the segmentation, not Button 2 as indicated. I didn't know what you meant by the "middle button", but I started to experiment and discovered it was Button 3 that paints the label. Thanks again for your help. Should I change this Wiki page to indicate that it is Button 3 or is this just an issue for those who use Macs with the new standard Mac mouse? Best,
Jared
freesurfer@nmr.mgh.harvard.edu
-
Jared Conley -
Jenni Pacheco -
Kevin Teich