thanx bruce,
Now in the list, last time I didn't looked at To, and CC.
FreeSurferColorLUT.txt file.
I just tried, 1032 ctx-lh-frontalpole, this is also same, 0 voxel.
FreeSurferColorLUT.txt ( 999 SUSPICIOUS
255 100 100 0) , so this means, after this entry.. all the listed regions are not yet included ? .
Infact I wanted to use these segmented thalamas regions, and
now when they are not there, I thought to take (frontal cortex,
posterioparietal, occiptal, motor, temporal regions ) and put them in
FSL diffusion based connectivity analysis, to segment thalamus
according to connectivity. But I am not able to locate all these
regions nicely, in FreeSurferColorLUT.txt file.
sorry, just wana ask some very basic questions. Is aseg.mgz only source to get regions out ?, and FreeSurferColorLUT.txt for label
info ? should I use anything else, to get these regions.
regards, vin
On Tue, Nov 11, 2008 at 12:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
no,
the aparc+aseg.mgz has some as does the wmparc.mgz. You should send
these questions to the list so Doug, Nick et al. can answer
On Mon, Nov 10, 2008 at 11:46 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>wrote:
yes, they are in there because we intend to do them and have started
messing around, but nothing serious yet
On Mon, 10 Nov 2008, vin wrote:
Thank you for prompt reply.
I was looking this file, and there was listing of thalamic nuclei, so I
thought it does.
$FREESURFER_HOME/FreeSurferColorLUT.txt
:)
have a nice day !!
vin
On Mon, Nov 10, 2008 at 11:23 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>wrote:
Hi Vin,
we don't currently segment any thalamic nuclei, although hope to do so in
the future.
cheers,
Bruce
On Mon, 10 Nov 2008, vin wrote:
*Hi Doug, *
*Greetings!! *
complete thalamus ROI extraction works, but when I tried segmented
thalamic
nuclei, than output file doesn't contain anything.
*>mri_binarize --i aseg.mgz --match 8001 --o thalamus_nuclei_fs.nii*
this how output looks like :
input aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output thalamus_nuclei_fs.nii
Binarizing based on matching values
nMatch 1
0 8001
binval 1
binvalnot 0
Found 0 values in range
mri_binarize done
should I choose some other file expect aseg.nii.gz ? to get thalamic
nuclie
.
thank you very much !!
vin
*
*
On Tue, Nov 4, 2008 at 4:42 PM, Doug Greve <greve@nmr.mgh.harvard.edu
wrote:
They are in aseg.mgz, you can extract them into a nifti file with
mri_binarize --i aseg.mgz --match 251 --o CC_Posterior.nii
251 is the code for CC Posterior (found in
$FREESURFER_HOME/FreeSurferColorLUT.txt)
doug
vin wrote:
hi,
I am trying to export segmented regions as NIFTI, and it works for the
regions like Thalamus whole. But when freesurfer finished autorecon,
than
it showed lot of sub regions for example : Thalamic sub regions and
also
CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus Callosum)
and...Mid
anterior and Anterior.
How I can get these sub regions. In which files they are stored, and
How
I
can extract them as NIFTI format.
any suggestion would be great !!
thank you very much ,
vin
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