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.eduwrote: 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.eduwrote:

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.eduwrote:

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 > > ------------------------------ > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps:// > mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Centergreve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > >