Hi Siewmin,
If you want to use non-diffusion images in TBSS, you may want to use
this script.
It runs almost exactly as tbss_non_FA:
1. Put all non_FA images into a directory (e.g. called MTR), where the
files should have the exact same name as in the "orig" directory.
2. Create a directory (e.g. called MTR_transforms) where you put all
the transformation files that take you from MTR space to diffusion
space (either FLIRT matrices or FNIRT warpfields)
!! The files in MTR_transforms should be named:
- blah_FA (exactly as the MTR files and orig files) if you are
using warpfields
- blah_FA.mat if you are using FLIRT to get to diffusion space.
The script will simply concatenate these transforms with the ones
created by TBSS, and run tbss_non_FA.
Cheers,
Saad.
On 24 May 2009, at 18:26, Siew-Min Gan wrote:
> Hi,
> I'd like to analyse the white and gray matter of the MTR images. I
> wonder if I can do voxel based analysis on the white matter of MTR
> images with TBSS by following the procedures for the nonFA images
> (i.e the ADC, L1,2) as described in the webpage.
> Similiarly, for the gray matter of the MTR images, would it be fine
> to use
> the FSL-VBM procedures on the MTR images?
> Is it possible to alter one of the FSL_VBM steps and also analyse the
> white matter?
>
> I would register the MTR images to the FA images, and the MTR to the
> T1
> images of the subjects for the two analysis beforehand.
>
> Thanks
>
> Siewmin
>
--
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
|