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Hi - I'm not quite sure I understand what you mean. Do you mean you want an accurate measure of the volume of white matter per hemisphere, and do not want this value to be influenced by a poor left/right split? You can make the split more accurate by using a more accurate registration to standard space (e.g. FNIRT).

Saad.


On 3 Mar 2011, at 20:46, zao liu wrote:

Hi, dear Saad,
Do you still remember a couple of months ago, I posted a message about how to separate left part and right part of white matter in the FSL group discussion? You replied me and told me a perfect method to separate them. But recently I found another question. I need to calculate an accurate value on the white matter, and the changes in size of white matter will significantly influence this value. I wanna know whether the method you told me would change the size of white matter or not.
 
I am quite appreciate for your reply.
 
Thanks in advance.
 
Best Regards,
Zao Liu

2010/12/8 Saad Jbabdi <[log in to unmask]>
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



--
Xuemei Lei
National Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China. 100875
Tel: +86-13269171259
==============================================
Welcome to visit my blog: www.mobiye.com


--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)












--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)