On 02/13/2006 03:37 PM, Fornito, Alexander wrote:
Ok,
I had a look under attributes and I saw the ROI I created, so I assume this is
correct.
I tried to create a new ROi under the attributes > area color tab named ???. This
got rid of the > WARNING: Paint names with no corresponding area colors:??? in the
shell but it highlighted the rest of the brain (outside the ROI).I could still not
visualize my ROI.
It's safe to just ignore this warning:
Paint names with no corresponding area colors:???
I've also noticed that in cases where I can visualize the ROI, only exposed
nodes are highlihted; nodes in the sulcal depths are not highlighted.
Let's clarify your Draw Borders settings:
Type: closed
Dimension: 2D (i.e., you're drawing on a flat map)
Closed border assignment:
Surfaces Nodes:
Assign Paint Identifiers to nodes within border checkbox is selected
Paint Column: -- what are you using here?
Reassign nodes with -- is this checked, and if so, what is selected?
I created my surfaces using the command line utlity.Maybe I've done something
wrong? My commands are below.
I've also noticed that alothough my left surface comes up in the correct
orientation, Caret confuses the medial and lateral surfaces for my right
hemispheres; when I press L it takes me to the medial view, and when I press M
it takes me to the lateral view. All other viewing conrtols seem to be correct.
Adding a line like this to your spec file will solve this problem:
hem_flag right
LEFT:
/usr/local/caret/bin/caret_file_convert -sc -is FSS lh.white.asc -os CARET
1000001.lh.white.coord 1000001.lh.closed.topo RAW CLOSED -spec 1000001.lh.spec
-hem LEFT
This looks good, except I have been using "left" instead of "LEFT";
also, I'm using smoothwm instead of white, but I don't have a strong
preference on this.
/usr/local/caret/bin/caret_file_convert -sc -is FSS lh.pial.asc -os CARET
1000001.lh.pial.coord 1000001.lh.closed.topo RAW CLOSED -spec 1000001.lh.spec
-hem LEFT
/usr/local/caret/bin/caret_command -surface-average 1000001.lh.FIDUCIAL.coord
1000001.lh.white.coord 1000001.lh.pial.coord
/usr/local/caret/bin/caret_command -volume-create 256 256 256 -128 -128 -128 1
1 1 RIA 1000001_segvol.hdr
I need to check with John Harwell on this; I'm guessing the origin is a
coordinate -- not a voxel index. I'm trying to get clarification from
some folks on the AFNI message board:
http://afni.nimh.nih.gov/afni/community/board/read.php?f=1&i=9128&t=9128
But this should get you in the ballpark.
/usr/local/caret/bin/caret_command -surface-to-segmentation-volume
1000001.lh.FIDUCIAL.coord 1000001.lh.closed.topo 1000001_segvol.hdr
/usr/local/caret/bin/caret_command -surface-identify-sulci 1000001.lh.spec left
1000001_segvol.hdr 1000001.lh.closed.topo 1000001.lh.FIDUCIAL.coord
1000001.lh.FIDUCIAL.coord
RIGHT:
/usr/local/caret/bin/caret_file_convert -sc -is FSS rh.white.asc -os CARET
1000001.rh.white.coord 1000001.rh.closed.topo RAW CLOSED -spec 1000001.rh.spec
-hem RIGHT
/usr/local/caret/bin/caret_file_convert -sc -is FSS rh.pial.asc -os CARET
1000001.rh.pial.coord 1000001.rh.closed.topo RAW CLOSED -spec 1000001.rh.spec
-hem RIGHT
/usr/local/caret/bin/caret_command -surface-average 1000001.rh.FIDUCIAL.coord
1000001.rh.white.coord 1000001.rh.pial.coord
/usr/local/caret/bin/caret_command -volume-create 256 256 256 -128 -128 -128 1
1 1 RIA 1000001_segvol.hdr
/usr/local/caret/bin/caret_command -surface-to-segmentation-volume
1000001.rh.FIDUCIAL.coord 1000001.rh.closed.topo 1000001_segvol.hdr
/usr/local/caret/bin/caret_command -surface-identify-sulci 1000001.rh.spec
right 1000001_segvol.hdr 1000001.rh.closed.topo 1000001.rh.FIDUCIAL.coord
1000001.rh.FIDUCIAL.coord
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of John Harwell
Sent: Tue 14/02/2006 5:43 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Viewing ROIs
On Feb 13, 2006, at 1:13 AM, Fornito, Alexander wrote:
Hi,
I seem to be able to view manually drawn ROIs with variable
consistency, and its causing me a bit of confusion.
For example, in the right hemisphere of one of my subjects, I draw
the ROI using Layers>Borders>Draw Border.
I then save the area color file and paint file, and when I check
the paint row in the D/C, I can see the ROI I drew.
If I repeat this process in the left hemisphere, I can't see it and
the shell I'm running Caret from returns the message:
WARNING: Paint names with no corresponding area colors:
???
I'm not sure why the same process would work for one hemisphere and
not the other. Note this also happens if I exit Caret and try to re-
load the area color and paint files.
Any help is much appreciated.
Thanks,
Alex
Alex,
When you assign a paint area, nodes that have not been identified by
the user are given the name "???" which implies that the nodes'
identities are unknown. The WARNING message is produced because
there is no color available for nodes with identity "???". You can
eliminate this message by adding a color for "???" by selecting Edit
from the Attributes:Area Colors menu. The lack of a color for "???"
should not affect the drawing of ROIs.
On the Surface:Region of Interest Dialog, make sure that you see
nodes appear in green after pressing the Select Nodes pushbutton to
select your region. When assigning the paint identifier, be sure to
provide a name for the nodes before pressing the Assign pushbutton.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
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