Maybe I'm missing something, but would mapping to volume from the
midthickness surface, with a thickness value greater than the maximum
cortical thickness value, and then masking with the ribbon volume give you
what you want?
Tim
On Wed, Jan 4, 2012 at 9:13 AM, Donna Dierker
of caret-users digest...
Today's Topics:
1. Re: caret-users Digest, Vol 100, Issue 2 (Timothy Coalson)
-- Forwarded message --
From: Timothy Coalson tsc...@mst.edu
To: Caret, SureFit, and SuMS software users
caret-users@brainvis.wustl.edu
Cc:
Date: Wed, 4 Jan 2012 14:28:27
with cytoarchitecure as paint.
On Fri, Feb 17, 2012 at 16:08, Timothy Coalson tsc...@mst.edu wrote:
We have moved away from the 73730 mesh, we are now using a new method to
generate meshes which results in much more regular node spacing. Making a
sphere is actually relatively easy, especially with the new
created after reconstruction from contours.
I think I understand how to make a standard spherical mesh but do I need
to make a standard fiducial mesh to allow intra and interspecies
registration?
Cheers,
Tristan
On Sat, Feb 18, 2012 at 05:31, Timothy Coalson tsc...@mst.edu wrote:
The new
I believe .ima is an extension used for dicom data, try a dicom to nifti
converter such as dinifti or dcm2nii (part of mricron).
Tim
On Fri, Mar 9, 2012 at 9:09 AM, Maestri, Matthew mmaes...@georgiahealth.edu
wrote:
Hi Donna,
Is it possible for me to open ima images in Caret? If not, is
-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker [
do...@brainvis.wustl.edu]
Sent: Friday, March 09, 2012 12:10 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] ima images
Try something like AFNI's to3d.
On Mar 9, 2012, at 11:04 AM, Timothy Coalson wrote
.
On Mar 12, 2012, at 3:59 PM, Timothy Coalson wrote:
FSL is another software package for viewing and manipulating MRI images,
etc, which is entirely separate from Caret:
http://www.fmrib.ox.ac.uk/fsl/
to3d's help suggests that it should understand .ima, but it doesn't seem to
give much detail
It looks like you are probably running centOS 5.7 or 5.8. Unfortunately,
the enterprise support model keeps old package versions around longer,
making it harder to build things to be compatible with them from other
distributions. We have moved to compiling on ubuntu, though we use an
older
Since what the myelin mapping maps is basically T1/T2, you may be able to
adjust your data to be in a plausible range for these values, and then fake
the T2 by taking an image that looks like a T1 and dividing it by this
adjusted data. As long as your data is not discontinuous at the edge of
the
I generally regard the average neighbors smoothing as a legacy
method, to be used only if you need to compare to a previous study
that also used it. The geodesic gaussian smoothing method in caret5
uses a gaussian kernel based on geodesic distance directly, so you
don't need to futz with the
Looks like a quoting problem to me. Your shell is interpreting
-surface-apply-transformation-matrix lh.white.coord.gii lh.white.topo.gii
as one argument, when it needs to be three. If these commands are run in a
script, quote each argument separately, rather than all together. If you
are
-apply-transformation-matrix
(Timothy Coalson)
--
Message: 1
Date: Thu, 13 Sep 2012 15:49:11 -0700
From: Andrew Bock ab...@u.washington.edu
Subject: [caret-users] caret_command
-surface-apply-transformation
One more thing to keep in mind, when you flip a surface's coordinates, the
normals will point inward rather than outward, so you may want to also
reorient the topology to have the normals outward
(-surface-topology-fix-orientation looks like the right command).
Tim
On Thu, Dec 6, 2012 at 11:38
flirt does not use the nifti origin, I think this may be the cause of your
problems. I wrote a utility to convert between simple coordinate to
coordinate matrices and the matrices flirt expects (and another convention
or two specific to 4dfp). You probably won't have it unless you have a
very
not uniform)?
Cheers,
Tristan
On Thu, Feb 21, 2013 at 8:56 AM, Timothy Coalson tsc...@mst.edu wrote:
The surface generated as the average of all subjects in the atlas is
significantly smoother than any individual's surface, which reduces
the surface area. This may account for the discrepancy
You may be able to trick the -surface-average command into doing this, if
the intermediate you want is a rational number, by providing the same
coordinate file multiple times to increase its weight (so if you wanted 3/8
versus 5/8, specify one file 3 times and the other 5 times). What do you
want
pulvinar is just a legacy alias for brainvis, the upload link should really
be http://brainvis.wustl.edu/cgi-bin/upload.cgi
I was hoping that one of the tools I mentioned was easily available, so
Irene could check the header directly.
As for getting plumb data through freesurfer, it may be best
testing list moderation settings
Tim
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Actually, it is probably more my area to answer this. Inline replies.
Tim
On Fri, Jun 14, 2013 at 1:40 PM, Colin Reveley cm...@sussex.ac.uk wrote:
Hi - I guess this is a question specificially for matt.
I have some FSL processed diffusion data. I want to display the mean fibre
orientations
Inline replies.
Tim
On Sun, Jul 14, 2013 at 12:23 PM, Colin Reveley cm...@sussex.ac.uk wrote:
Hi - I have a few questions about WB functionality and plans for
functionality
a) what is the position on flatmaps? can these be displayed (e.g. made in
CARET5, saved as surf.gii, will they work?
Warping the vertices should not need to change the faces, so that shouldn't
be a problem. That scrambling makes me wonder if something is getting the
endianness wrong, are the values extremely large?
If you can put your warpfield into a 3-brick nifti volume, with format of
relative x, y, and z
It should compute it one row at a time, so as long as you have enough rows
that it divides the total cifti file into a managable row size, you should
be fine. You can always try it on your local machine, and see if it starts
allocating swap (cifti-math, along with the other math commands, aren't
From what I remember of the issue, some JREs were holding onto memory that
should have been deallocated, which eventually fills the memory pool and
crashes, while the good JREs kept their memory usage fairly constant. The
issue was solved in Sun's java before the default java debian/ubuntu
You don't use your email as the user, you use the login name from the
registration email (right above the password).
Tim
On Wed, Jan 29, 2014 at 4:14 PM, Ping-Hong Yeh pinghong...@gmail.comwrote:
Hi Caret Users,
I was not able to login to access the Myelin_Mapping_Documentation_v2.doc
Subject: Re: [caret-users] libstdc++ version and caret5
To: John Harwell j...@brainvis.wustl.edu
Cc: Donna Dierker do...@brainvis.wustl.edu, David Van Essen
vanes...@wustl.edu, Timothy Coalson tsc...@mst.edu
Hi John,
thank you very much!
To a first approximation, the Redhat version you provide
Completely removing sform and qform will result in a volume with
coordinates (0, 0, 0) at a corner of the FOV, this is almost certainly not
what you want. What you probably want is the sform and qform to both be
valid, and to match, and the matrix to have zeros except on the diagonal
and last
wb_command -metric-smoothing does have better smoothing methods,
particularly GEO_GAUSS_AREA, which takes into account variation in vertex
area.
You will also need to rename the converted file to something.func.gii if
you want to view it in workbench rather than caret.
I would also suspect that
see, dim3 is different than the T1 and T2. But I used the command
the command that was mentioned in the instruction to generate ribbon (i.e.
mri_convert
-rl mri/rawavg.mgz mri/ribbon.mgz ribbon.nii.gz).
Any suggestion how to correct this problem?
On Thu, Jul 31, 2014 at 3:08 PM, Timothy
the vertices in surf.gii and the voxel in fMRI. Please help me.
Thank you.
--
*From:* caret-users-boun...@brainvis.wustl.edu [
caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [
tsc...@mst.edu]
*Sent:* Wednesday, August 06, 2014 1:27 PM
*To:* Caret
On Mon, Aug 11, 2014 at 2:14 PM, Tang, Yan yan.t...@ttu.edu wrote:
Yes，I have a lot of volumes which need be projected to surface. I only
know how to use the 'map volume to surface '. I don't know how to use the
command. Could you give me an example?
Can the file of *.coord.gii be thought as
-boun...@brainvis.wustl.edu [
caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [
tsc...@mst.edu]
Sent: Tuesday, August 12, 2014 7:16 PM
To: Caret, SureFit, and SuMS software users; Donna Dierker
Subject: Re: [caret-users] projecting functional MRI to gii surfaces
-spec
files to Workbench
format by using wb_import. Is it true?
From: caret-users-boun...@brainvis.wustl.edu [
caret-users-boun...@brainvis.wustl.edu] on behalf of Timothy Coalson [
tsc...@mst.edu]
Sent: Tuesday, August 12, 2014 7:16 PM
To: Caret, SureFit, and SuMS software users; Donna Dierker
The script quoted in the post you linked specifically resamples the
surface, so if that is what you did, the output from it is the midthickness
in fs_LR32k. Other surface types can be resampled the same way. Caret5
will load .surf.gii files just fine, you don't need to convert back to
topo/coord
I think caret5 has trouble with non-english locales, if you are using a
different OS language, could you try setting the OS language to english and
trying it again?
Tim
On Fri, Jan 9, 2015 at 1:18 AM, 陈晨 chenchen_...@163.com wrote:
ChenChen
chenchen_...@163.com
caret5
v5.65 AND Jan 27
For coord files, I would use them and a topo file with caret_command
-file-convert -sc and make a gifti surface file. For a paint file, I would
see about converting it to a gifti label file ".label.gii". Gifti file
types can be loaded with the gifti matlab toolbox:
in
anatomical size of various features of the cortex.
Since you were talking about "deformation from native space to fs_LR", I
didn't think about these other possibilities.
Tim
On Fri, Oct 20, 2017 at 5:59 PM, Timothy Coalson <tsc...@mst.edu> wrote:
> Deformation maps are
Deformation maps are inherently designed for the purpose of going from one
topology (number of triangles and their layout) to a different one, so they
are a tricky thing to try to compare vertexwise. They also don't really
encode warpfield deformations (and even using them to reconstruct as much
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