Hi Paul, Thank you again for your reply.
My target is to create right hemishphere mask using my T1 image
Kindly, how I should use fslmaths -roi to do so?
Sincerely
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of paul mccarthy [[log in to unmask]]
Sent: Friday, June 13, 2014 5:34 AM
To: [log in to unmask]
Subject: Re: [FSL] Brain Rigt left hemisphere segmentation
Hi M.,
If you just want to create hemisphere masks, you can do that easily with fslmaths (see the '-roi' option).
Otherwise, the easiest way to get anatomical labels for the voxels of a T1 image is to register that image to the MNI152 atlas using FNIRT, and then use the labels from one of the atlases which come with FSL, e.g. the Harvard-Oxford cortical atlas, or the MNI atlas.
These are stored in $FSLDIR/data/atlases/, and are accessible in FSLView via Tools->Toolbars->Atlas tools.
If you want detailed cortical segmentation, you'll probably have to look at something like Freesurfer.
Hope that helps,
Paul
On Thu, Jun 12, 2014 at 8:14 PM, M. alshikho <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi FSL Experts;
The default output of FAST tool in FSL is for GM, WM, and CSF. What is the preferred method for further segmentation? For example, to output right hemisphere and left hemisphere GM and WM, frontal cortex GM and WM, etc?
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