Thanks Donna!
On Fri, Jan 15, 2016 at 3:07 AM, Donna Dierker
wrote:
> Hi Rosita,
>
> It can be so frustrating. Sounds like you have some good alternatives to
> explore.
>
> This link details one user's alignment issues and the solution:
>
> http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html
Hi Rosita,
It can be so frustrating. Sounds like you have some good alternatives to
explore.
This link details one user's alignment issues and the solution:
http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html
login pub
password download
Donna
On Jan 13, 2016, at 10:09 PM, Rosita Shisheg
Hi Donna,
Thanks for the explanation.
Unfortunately, as a result of preprocessing steps my surfaces are
transformed, resized, and they are not even aligned with the original
volumes anymore and I prefer not to bother with registration with original
data.
The final goal was to compute sulcal dept
Hi Rosita,
None of the parameters in these commands makes sense for sheep:
> caret_command -volume-create 176 208 176 hull_vol.nii
volume dimensions
> caret_command -volume-set-origin hull_vol.nii hull_vol.nii -88.0 -123.0 -75.0
volume origin
> caret_command -volume-set-spacing hull_vol.nii hull_
Hi Donna,
Thanks a lot for the help.
I ran the commands as you suggested and now I can compute the volume and
the hull. My understanding is that the inputs that you chose for creating
volume (*-volume-create** 176 208 176* ) and the origin (
*-volume-set-origin* hull_vol.nii hull_vol.nii *-88.0
Thanks for offering help Donna!
I uploaded the surface *.stl and its converted version to *.pial that I
used as the input for Caret.
The folder also include a text file containing commands that I used. For
some reason I can not run caret commands in my terminal so I use caret
command executor. So
Upload a zip file containing the script (or just email commands used) and the
inputs (surface or segmentation) here:
http://brainvis.wustl.edu/cgi-bin/upload.cgi
I'll have a look.
On Jan 5, 2016, at 12:31 AM, Rosita Shishegar
wrote:
> Hi Donna and all caret users,
>
> Happy new year!
>
>
Hi Donna and all caret users,
Happy new year!
Before, I asked about computing sulcal depth from the cortical surface.
Donna suggested that I use gen_depth.sh file as a guide.
Using the commands, first I tried to create the volume from the surface
which later I needed for computing hull and the s
Hi Rosita,
This zip archive has a script named gen_depth.sh:
brainmap.wustl.edu/pub/donna/US/UCDAVIS/cwn.zip
login pub
password download
You'll need to adapt it to your data, but it will give you a head start.
Donna
On Sep 2, 2015, at 7:01 PM, Rosita Shishegar
wrote:
> Hi,
>
>
> I am a
Hi,
I am a new Caret user and I am working on animal brain data, which are
manually segmented and triangulated mesh of cortical surface is already
extracted and pre-processed.
I want to measure Sulcal Depth of theses brains and so I need to generate
Cerebral Hull surface of them. Is there any
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