yeah, those two buttons are too close to each other aren't they? :)
saad.
On 8 Dec 2010, at 14:24, Evangelou, Iordanis (NIH/NINDS) [E] wrote:
> Saad
>
> I think tsize in -roi needs to be 0 and not 9
>
> Iordanis
>
>
> -------------------------------------------------------------------
> Iordanis E. Evangelou, DPhil
> Staff Scientist
> Neuroimmunology Branch
> National Institute of Neurological Disorders and Stroke
> National Institutes of Health
> Building 10, Room 5C103
> Bethesda, MD 20892
>
>
>
>
>
> On 12/8/10 4:56 AM, "Saad Jbabdi" <[log in to unmask]> wrote:
>
> Hi
> You can roughly left/right split the brain very easily after registering to MNI standard space. You can do it in your original space by splitting a standard space mask and resampling it into your original space (standard space splits at x=45 in 2mm, so very easy to do).
>
> For example, if you want the right hemisphere:
>
> fslmaths $FSLDIR/data/standard/MNI152_T1_2mm -mul 0 -add 1 -roi 0 45 0 109 0 91 9 1 rightvol
> flirt -in rightvol -out rightvol_orig -ref <origvol> -applyxfm -init <standard2orig.mat> -interp nearestneighbour
> fslmaths <origvol> -mas rightvol <origvol_right>
>
>
> Saad.
>
>
> On 7 Dec 2010, at 19:10, zao liu wrote:
>
> Hi,
> Thanks. But the MNI template size is smaller than the data I am using. And I do not want to reduce the image size, since it will influent the results. Is it possible that, I draw a circle in ROI in the upper slice, and apply this circle into the few lower slices using simple copy and paste?
>
> Best Regard,
>
> Zao Liu
>
> 2010/12/5 xuemei lei <[log in to unmask]>
> Hi,
> there are right and left WM atlas in the HarvardOxford-Subcortical templates. Maybe you could use that atlas to mask you images. But first you should register them.
>
> Good luck
>
> Xuemei
>
>
> On Mon, Dec 6, 2010 at 7:36 AM, zao liu <[log in to unmask]> wrote:
> Dear all,
> I am new to FSL.
> Now, I am trying to separate the left and right parts of the brain. How can I extract left part from the whole white matter in one slice, and apply it in all slices?
>
> Thanks a lot.
>
> Zao Liu
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
|