Re: [Freesurfer] Getting voxel values from aseg.mgz

[Douglas N Greve]

You can also use mri_binarize which has more documentation :-)

On 12/11/2014 01:31 AM, pradeep mahato wrote:
> There is no documentation or example for mri_extract_label.
> What should be the syntax for it. What kernel and xform file should be 
> used.
>
> On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Pradeep
>
> you can use mri_extract_label to copy just the hippocampal labels
> out of
> the segmentation if that is what you mean. The values for left and
> right
> hippocampus (17 and 53) can be found in
> $FREESURFER_HOME/FreeSurferColorLUT.txt
>
> cheers
> Bruce
> On
> Wed, 10 Dec 2014, pradeep mahato wrote:
>
> > After the recon-all process I want to access all the voxels in
> the left
> > hippocampus ( any subcortical region ) .
> > Please tell me is there any method to extract this voxel values
> from an
> > segmented image.
> >
> > Thanking you
> >
> > Pradeep Kumar Mahato
> >
> >
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>
>
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>
>
>
> -- 
> Pradeep Kumar Mahato
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] Getting voxel values from aseg.mgz

[Bruce Fischl]

  mri_extract_label
Usage: mri_extract_label [options]... 

Options:
-s   apply a Gaussian smoothing kernel
-t  apply the transform in  to extracted 
volume
-exit_none_foundexit 1 if label(s) not found
-dilate  dilate output volume  times
-erode   erode output volume  times

This program will extract a set of labeled voxels from an image.


so from the subject's mri dir you could do:

mri_extract_label aseg.mgz 17 53 hippo_labels.mgz

cheers
Bruce

On Thu, 11 
Dec 
2014, pradeep mahato wrote:

> There is no documentation or example for mri_extract_label.
> What should be the syntax for it. What kernel and xform file should be used.
> 
> On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl 
> wrote:
>   Hi Pradeep
>
>   you can use mri_extract_label to copy just the hippocampal
>   labels out of
>   the segmentation if that is what you mean. The values for left
>   and right
>   hippocampus (17 and 53) can be found in
>   $FREESURFER_HOME/FreeSurferColorLUT.txt
>
>   cheers
>   Bruce
>   On
>   Wed, 10 Dec 2014, pradeep mahato wrote:
>
>   > After the recon-all process I want to access all the voxels in
>   the left
>   > hippocampus ( any subcortical region ) .
>   > Please tell me is there any method to extract this voxel
>   values from an
>   > segmented image.
>   >
>   > Thanking you
>   >
>   > Pradeep Kumar Mahato
>   >
>   >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
> 
> 
> 
> 
> --
> Pradeep Kumar Mahato
> 
>
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Re: [Freesurfer] Getting voxel values from aseg.mgz

[pradeep mahato]

There is no documentation or example for mri_extract_label.
What should be the syntax for it. What kernel and xform file should be used.

On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl 
wrote:

> Hi Pradeep
>
> you can use mri_extract_label to copy just the hippocampal labels out of
> the segmentation if that is what you mean. The values for left and right
> hippocampus (17 and 53) can be found in
> $FREESURFER_HOME/FreeSurferColorLUT.txt
>
> cheers
> Bruce
> On
> Wed, 10 Dec 2014, pradeep mahato wrote:
>
> > After the recon-all process I want to access all the voxels in the left
> > hippocampus ( any subcortical region ) .
> > Please tell me is there any method to extract this voxel values from an
> > segmented image.
> >
> > Thanking you
> >
> > Pradeep Kumar Mahato
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Pradeep Kumar Mahato
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Re: [Freesurfer] Getting voxel values from aseg.mgz

[Bruce Fischl]

Hi Pradeep

you can use mri_extract_label to copy just the hippocampal labels out of 
the segmentation if that is what you mean. The values for left and right 
hippocampus (17 and 53) can be found in 
$FREESURFER_HOME/FreeSurferColorLUT.txt

cheers
Bruce
On 
Wed, 10 Dec 2014, pradeep mahato wrote:

> After the recon-all process I want to access all the voxels in the left
> hippocampus ( any subcortical region ) .
> Please tell me is there any method to extract this voxel values from an
> segmented image.
> 
> Thanking you
> 
> Pradeep Kumar Mahato
> 
>
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[Freesurfer] Getting voxel values from aseg.mgz

[pradeep mahato]

After the recon-all process I want to access all the voxels in the left
hippocampus ( any subcortical region ) .
Please tell me is there any method to extract this voxel values from an
segmented image.

Thanking you

Pradeep Kumar Mahato
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