Dear Mark,
Suppose I used faslmaths -roi correctly and have the results in hand as brain_roi.which on of these codes give me the volume of the brain_roi:
fslstats brain_roi –M –V | awk ‘{print $1 * $3}’or
fslstats brain_roi –M –V | awk ‘{print $3}’
and what would be the units for that volume ?
Thank you,
Mahmoud
On Sat, Oct 25, 2014 at 1:57 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,
I'm not 100% sure what the exact calculation is that you are trying to do, but often asymmetries are calculated by taking the images and registering them to a symmetric standard space template, and then flipping the image in the template space to compare things between left and right in a voxel-wise manner.
If you want to calculate left and right summaries instead, then the image after registration to the template can be easily masked using the -roi option in fslmaths. For example, with the 1mm MNI templates you would use:
fslmaths <my_image> -roi 0 91 0 -1 0 -1 0 1 <my_image_right>
fslmaths <my_image> -roi 91 91 0 -1 0 -1 0 1 <my_image_left>
For other templates or other resolutions you'd need to modify these numbers.
All the best,
Mark
On 24 Oct 2014, at 19:31, Mahmoud <[log in to unmask]> wrote:
> Dear all,
>
> Can anyone let me know how to compute the brain tissue asymmetry index using FSL ?
> I need to have the separated index for CSF, GM and WM.
>
> Thank you,
> Mahmoud