Dear Caret users,
While it is a trivial thing, I noticed that right-mouse click won't
show up the pop up menu in the surface volume view or volume view.
However, right-mouse click works for other views. Could it be a bug for
the window version or it was designed to be that way.
Let me
that you would like to replace. Move the mouse so that it
is over the starting location of the border segment that you would like to
replace. Hold down the left mouse button and move the mouse to draw the new
border segment and continue until the new segment touches the end of the
existing segment
border that you would like to replace.
Move the mouse so that it is over the starting location of the
border segment that you would like to replace. Hold down the left
mouse button and move the mouse to draw the new border segment and
continue until the new segment touches the end
-mouse click won't
show up the pop up menu in the surface volume view or volume view.
However, right-mouse click works for other views. Could it be a bug for
the window version or it was designed to be that way.
Let me know.
Thanks,
YSL
the segment of
the
existing border that you would like to replace. Move the mouse so that
it
is over the starting location of the border segment that you would like
to
replace. Hold down the left mouse button and move the mouse to draw the
new
border segment and continue until the new
inverse transform for? I think I understand the
Here is a copy of the documentation I wrote so that I am able to
generate these transforms in the future:
I read that again tomorrow.
Bugs:
Whishlist. Would it be possible in mouse mode to use the middle and
right
button additionally to shift
and that white matter be brighter on average and CSF be
darker.
The hindbrain and cerebellum need customized handling that is
species-specific; this is also the case for the olfactory bulb in
rodents.
The segmentations of mouse and rat cerebral cortex that are the basis
of our rodent surface
of the border you're
unhappy with, and then drag (hold down with left mouse button while
moving the mouse) along the desired trajectory, until you want the
border to stop. Then shift-click to terminate.
Is that what you meant by hoover?
On 08/05/2010 05:19 AM, j janssen wrote:
Hi,
- version
the CaSu nearly stretch to the most ventral extent of the surface?
also, a separate problem is that when i press the apply button in the DRAW
Borders dialog and begin to click the left mouse button to trace the medial
wall on the surface in the main window, it doesn't show me a border being
drawn
Hello Caret users,
Has anyone experience problems with loading area color files (user created) and
having Caret store them for future use? I seem to always need to open manage
loaded files and remove the color file before loading a new one, even if I
load the same area color file it saves an
, it was unchecked, but I'm wondering what it
exactly is for. Any help would be appreciated.
Some of the user-interface components provide tooltips including the
Apply RGB paint L If you place the mouse over a control and do
not move the mouse for a few seconds a tooltip appears describing
that there are duplicated borders.
Press the IDB button in the toolbar (enabled identification of
borders), and then click the mouse over a border. If after a mouse
click, two borders with the same name are found, then you have found
your overlapping borders. Use Layers:Borders:Delete Border with Mouse
, they are displayed at a lower resolution (even when the display
window is maximized), causing some of the grid lines to fade or disappear,
and making it difficult to see features of the smaller slices for tracing.
Zooming using the middle mouse button in View mode doesn't seem to affect
the resolution
Hi Brige,
I am not someone who has had success (or failures) with mouse brain
segmentation, but I tried segmenting the map015 left hemisphere using
Caret, just to see what would happen. I made these selections:
* left the voxel size at 0.056mm
* GMpeak=45 ; WMpeak 60
* toggled off
.
* On the display control's CoCoMac page, set the Paint Column to
Functional.
* Click the mouse on the brain and the functional area is shown in red
and connected areas are shown in green.
---
John Harwell
[EMAIL PROTECTED]
Department of Anatomy and Neurobiology
Traci,
I don't understand why the message below bounced. Nor do I really
understand how the paint indices got mixed up.
But you should not need to re-draw the medial wall. Do this:
Surface: Region of interest, selection source Paint, select Brodmann.40
Select node with Mouse, and click
-Segmentation - Edit voxels - say turn
voxels off . After that, when I try to move my cursor ( left mouse
pressed) over the volume and nothing happens. There is no change in the
red colored Overlay. It is as if there my action to edit voxels did not
occur at all. I am using a 64 bit Linux
Michael,
You can zoom the Volume Montage just like a single slice view (Hold down CTRL
Key while moving mouse forward). It may partially clip the volumes. You could
also change the background color (File Menu-Preferences) so that it matches
the background color in the volume slices).
John
mouse was not effective for any action.
System beep
sound was generated in response to mouse clicking. There was no
way to do,
so I had to turn off the PC by using the hardware switch.
I set the CARET_HOME at C:\Program Files\caret where I installed
caret.
Any suggestions to sart up
in the
border update mode.
In the example image, you should use the Replace Segment option. Start near
the yellow contour to 'latch' onto the corpus callosum, then run your mouse
over to the callosum and follow the trail, but also you need to end up close to
the selected border. After completing this step
button.
4) Place the mouse over the lesion, hold down the left mouse button
and move the mouse so that the lesion is covered with segmentation
voxels (dark red color).
5) Increment to the next slice containing the lesion.
6) Repeat steps 45.
7) Save the Segmentation Volume using File Menu-Save
for caret log
messages).
So I left it overnight and then came back. But I could not drag any of
caret windows and my mouse was not effective for any action. System beep
sound was generated in response to mouse clicking. There was no way to
do,
so I had to turn off the PC by using the hardware
:
Visualization and Data-Mining using Caret, WebCaret, and SumsDB
Software | J Harwell, D Van Essen, J Dickson, D Dierker
1.30 pm – 4.30 pm | GeneNetwork, The Mouse Brain Library, and a new
Atlas of the Developing Mouse Brain | RW Williams, W Bug, A Centeno,
J Nissanov, KF Manly, GD Rosen
your mouse
over to the callosum and follow the trail, but also you need to end up close
to the selected border. After completing this step (by shift-click), carry
out the remaining edits using replace, erase, or extend, as appropriate.
Hope this helps.
David VE
On Jul 18, 2012, at 4:38 PM
quit at the Matlab prompt to exit Matlab.
Bugs:
Whishlist. Would it be possible in mouse mode to use the middle and
right
button additionally to shift/ctrl left button for panning and zooming?
I
think it was that way in caret 4 and found it very practical.
That is the way it used
lines to fade or disappear,
and making it difficult to see features of the smaller slices for tracing.
Zooming using the middle mouse button in View mode doesn't seem to
affect
the resolution of the slice images. Are there any options for adjusting
the
scale at which the images are displayed
trying to draw the medial
wall borders. When I open the draw borders dialogue, choose the
border name, set type to closed and dimension to 2D, and press
apply, I can't draw the border. I click on the sphere and hold the
left mouse button and nothing is drawn. Any ideas on what's going
- Edit voxels - say turn
voxels off . After that, when I try to move my cursor ( left mouse
pressed) over the volume and nothing happens. There is no change in the
red colored Overlay. It is as if there my action to edit voxels did not
occur at all. I am using a 64 bit Linux Machine. I tried
just like a single slice view (Hold down CTRL
Key while moving mouse forward). It may partially clip the volumes. You
could also change the background color (File Menu-Preferences) so that it
matches the background color in the volume slices).
John
On Jan 11, 2011, at 2:46 PM, Michael
I haven't noticed this particular problem. Using Toolbar: Spec and opening the
desired area color, choosing Replace when prompted, might be easier (or might
not).
But what I have noticed is that even after I open the right area color file and
replace, and save a scene with that area color
to toggle voxels mode, zoom/pan the surface so you can
get the best view of the fused area. Then, press the toggle voxels
button on the patching menu. The right mouse button toggles voxels off,
left on. In the case of the calcarine fuse, sagittal slices 19-31 were
affected, so start at 19 or 31
end. I'm not sure I understand what you mean. (Some
captures with well-placed ID nodes will help me get it if my captures
don't clear things up.)
also, a separate problem is that when i press the apply button in the
DRAW Borders dialog and begin to click the left mouse button to trace
: Region of interest, selection source Paint, select Brodmann.
40
Select node with Mouse, and click in the medial wall.
Press select nodes and then Remove Islands
Next
Assign Paint: Column Brodmann
Assign Name MEDIAL.WALL
File: Save Data File: Paint
Donna
Original Message
the corresponding locations on the initial flat map.
Some reminders:
* To get rid of the green ID boxes/spheres, hold down your right mouse
button and select clear ID.
* If you were in Draw Cuts mode, you can switch back to ID mode by
pressing the View button on the main caret window.
It's easy to see where
to normal and than back
to individual? Obviously 2 transformation are worse than none. So I guess
there must be some application I for this method. As I use caret as a
flattening tool to spm I am just curious.
Bugs:
Whishlist. Would it be possible in mouse mode to use the middle and right
button
none. So I guess
there must be some application I for this method. As I use caret as a
flattening tool to spm I am just curious.
Bugs:
Whishlist. Would it be possible in mouse mode to use the middle and right
button additionally to shift/ctrl left button for panning and zooming? I
think
is on the flat map. Next, hold down the right mouse
button in the main caret window and clear the id nodes. Switch to a
posterior view in the inflated surface, and click on nodes on the
occipital pole. Now you can see where these nodes appear on the flat
map. Repeat this process in each region
right after the EndHeader line. If you don't delete from the end, then
you'll need to reindex the border numbers. Typically, if you use the
text editor to find the dup borders, it's easier to then use Layers:
Borders: Delete border with mouse to delete the top one.
Problems like this can occur
loaded.
2. Project the borders drawn on the flat map; save as borderproj.
3. Switch to inflated view.
4. Toolbar: spec: borderproj: and select your
*FromFlattening*borderproj; APPEND.
5. Use Layers: Borders: Delete border point with mouse to delete as
many points as needed to remove doubts about
on the sphere and hold
the left mouse button and nothing is drawn. Any ideas on what's
going on? I checked the D/C to see if show borders was selected
and it is. I've drawn borders in the past with no trouble, so I'm
not sure what's happening here.
Also, what does it mean in the Flatten Full
Hi Bayle,
Your problem replicates on my end -- i.e., I get an empty volume when I
view test.nii in Caret (see test.nii.caret.jpg).
When I view it in AFNI, I do see something that might be mouse cortex
(see test.nii.afni.jpg).
The header does look unusual. Here is AFNI's 3dinfo output
+
From:Baylis Shanks
To: Caret, SureFit, and SuMS software users
hi,
thanks for looking into it.
When I view it in AFNI, I do see something that might be mouse cortex
yes, it's mouse cortex, and that is what it is supposed to look
like :)
R-to-L extent: 5688.600 [L
into it.
When I view it in AFNI, I do see something that might be mouse
cortex
yes, it's mouse cortex, and that is what it is supposed to look
like :)
R-to-L extent: 5688.600 [L] -to- 5700.000 [L] -step- 0.200 mm
[ 58
voxels]
A-to-P extent: 7786.800 [P] -to- 7800.000 [P] -step- 0.200 mm
, this is because
we are multi-tasking on many atlas and other fronts; it is a challenge
to keep the atlas datasets reasonably current for human, macaque, rat,
and mouse in the face of software refinements along with additional
data that is good to bring into the atlas framework.
Feedback
,
and press apply, I can't draw the border. I click on the sphere
and hold the left mouse button and nothing is drawn. Any ideas
on what's going on? I checked the D/C to see if show borders
was selected and it is. I've drawn borders in the past with no
trouble, so I'm not sure what's
stuck trying to draw the medial
wall borders. When I open the draw borders dialogue, choose the
border name, set type to closed and dimension to 2D, and press
apply, I can't draw the border. I click on the sphere and hold the
left mouse button and nothing is drawn. Any ideas on what's going
understand why the message below bounced. Nor do I really
understand how the paint indices got mixed up.
But you should not need to re-draw the medial wall. Do this:
Surface: Region of interest, selection source Paint, select Brodmann.40
Select node with Mouse, and click in the medial wall
graphics
chip, Caret runs horrendously slow (editing voxels, node IDs, right mouse
button, etc.). However, when I change to the Nvidia chip, Caret runs fine. My
best guess is, that Caret and the HD4000 chip don't play nice together.
It would be interesting to see, if the other guys that experience
to draw the medial wall borders. When I open the draw borders
dialogue, choose the border name, set type to closed and
dimension to 2D, and press apply, I can't draw the border. I
click on the sphere and hold the left mouse button and nothing
is drawn. Any ideas on what's going on? I
node with Mouse, and click in the medial wall.
Press select nodes and then Remove Islands
Next
Assign Paint: Column Brodmann
Assign Name MEDIAL.WALL
File: Save Data File: Paint
Donna
Original Message
Subject:
MedialWall and BA40
From:
Sandoval, Traci I traci.sando
, and installed that one on my current system. When I'm using the HD4000
graphics chip, Caret runs horrendously slow (editing voxels, node IDs, right
mouse button, etc.). However, when I change to the Nvidia chip, Caret runs
fine. My best guess is, that Caret and the HD4000 chip don't play nice
together
v5.65 I installed on the 2nd gen
i3, and installed that one on my current system. When I'm using the HD4000
graphics chip, Caret runs horrendously slow (editing voxels, node IDs, right
mouse button, etc.). However, when I change to the Nvidia chip, Caret runs
fine. My best guess is, that Caret
chip, Caret runs horrendously slow (editing voxels, node IDs,
right mouse button, etc.). However, when I change to the Nvidia chip, Caret
runs fine. My best guess is, that Caret and the HD4000 chip don't play nice
together.
It would be interesting to see, if the other guys that experience
Hi Marc,
Yes -- make sure your surface shape column is set to Folding and cut
along the fundus of the sulcus outward toward the perimeter of the
surface. Don't forget to terminate the cut by holding down the shift
key and clicking the left mouse button.
Your segmentation still had
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