Print

Print
Hi Saad,

could you explain the general idea and steps on how to use tractography for the comparison of tracts in both hemispheres.
What do you mean by anatomically matching tracts of interest
Do you mean 
1) identify e.g. the Inferior Longitudinal Fascicle with tractography (using a combination of masks)
2) use this identified tract to generate a mask to be laid upon e.g. the FA-map
3) extract e.g. the FA-values just for this tract
4) compare them

Am I here on a totally wrong track?

thanks, michael


On 26-Sep-08, at 3:17 AM, Saad Jbabdi wrote:

Hi
This command:
fslmaths <input file> -roi 0 45 0 109 0 91 0 1 <output file>
will empty anything that is not in the right hemisphere (only works in standard MNI152 space).
You may adapt it to work for left hemisphere, and/or other spaces (diffusion/structural, etc.).

Coming back to your original question on how to match locations from both hemisphere for comparison, a good way to do that is with tractography. If you have a good knowledge of the white matter tracts that you want to compare, and a reproducible way of extracting them, then you may select "tracts of interest" from both hemispheres that would be anatomically matched, and suitable for statistical testings.

Cheers,
Saad.



On 26 Sep 2008, at 03:51, kirsten sash wrote:

Hi Michael,
Yup, looked at the paper. but how does one separate the hemispheres as mentioned in the paper. Sorry if this is has an obvious answer, but this is the first time I am using the FSL/TBSS stream for analyzing the data.

Kirsten

On Thu, Sep 25, 2008 at 5:40 PM, Michael Scheel <[log in to unmask]> wrote:
Hi Kirsten, did you have a look at the Buechel paper. I cannot for sure remember but I think they describe their approach quite in detail and it sounded very reasonable. Please let me know how about the progress. I will have a look at it again as well.

cheers, michael

kirsten sash schrieb:
Hi Michael,
Thank you for your response

Well, I ran the tbss scripts successfully. As far as the statistics are concerned, I did an inter group FA comparison
randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 -c 3 -V

But am not sure how to tease out the asymmetry differences if any. Do you have any suggestions ?

Thanks
Kirsten

On Sun, Sep 21, 2008 at 1:23 AM, Michael Scheel <[log in to unmask] <mailto:[log in to unmask]>> wrote:

   Hi Kirsten,

   any progress in your project?

   Have a look at the FDT, there is the processing streamline
   explained. You might want to check the second part of the fsl course
   and the practical on FDT. I started doing diffusion imaging also
   very recently and found the practical very useful.

   Are you familiar with the Buechel 2004 paper describing right and
   left FA difference for the Fasciculus arcuatus. This might be a good
   start although Buechel uses a VBM approach. FSL users probably
   suggest using TBSS, although I don't know how you would approach
   such a question with TBSS.



   Michael

   kirsten sash schrieb:


          Hi All,
          I am a newbie to FSL and was wondering if I could get some
       help with
          my analysis stream. I am hoping to calculate hemispheric
       differences
          in my subjects. At this point I have not segmented the T1
       brains and
          wanted to know if there was a way to analyze the DTI data. I have
          carried out the initial basic steps but do not know how to
       proceed
          after running dtifit. Any help is appreciated.

          Thanks !
          Kirsten Sash
          Arizona State University




--
Michael Scheel
AG PD Dr. Stroehle
Klinik fuer Psychiatrie und Psychotheraphie
Charite - Campus Charite Mitte
[log in to unmask]
0176 - 20801852


---------------------------------------------------------------------------
Saad Jbabdi, 
Postdoctoral Research Assistant,  
Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222545  (fax 222717)
---------------------------------------------------------------------------