> Dear Friends:
>
> I'm learning how to analyze DTI data with FSL(FDT), and I'm wondering
> if any one can make comments about my procedures described below.
>
> My DTI data were acquired with a Simens Trio 3T scanner. 32
> directions. b=1000
>
> (I) Use MRIconvert to convert the DICOM data into NIFTI format for
> DTI. The conversion created
> 1. one textile file with bvalues
> 2. one textile file with bvecs
> 3. one image file with b0
> 4. 32 image files with b1000

Please make sure you view the data first with FSLVIEW.  Mind particularly
the A-P orientation.
FSL is very picky on orientation.

MRIConvert can take care of the A-P orient issue of you choose your output
to be fsl_nifti, not nifti though.

>
> My question here is: Do I need to do any thing with the number in the
> bvalues and bvecs file before using the two files, e.g., normalize?

You do not normalize bvals, it is just weighting.

As for bvecs, I think MRIConvert will take care of the normalization
process, one way to check it is to square each number in a particular
column to see if they add up to 1.
for example, the XYZ numbers in column two:
0.8944
0
-0.4473
0.8944^2 + 0^2 + (-0.4473)^2 =1


>
> (II) Use fslmerge to merge all image files into 4D file. The 4D file
> has 33 images, and the b0 image is the first one.  Now I remove all 3D
> image files from the directory, so that the directory has 3 files
> left, one for bvalues, one for bvecs, one for 4D images.

yep

>
> (III) Rename the three files, so that their names are: set00_bvalus,
> set00_bvecs, set00_data.nii.gz
> My question here is: how strict is this rule for file naming?

In my memory, naming is not important at all if you are running command in
FSL (I like command lines better).
DTIfit GUI will automatically recognize each data if you have a specific
naming, but you can also manually choose each file.

>
> (IV) Use FDT to do Eddy current correction. The input file is
> set00_data.nii.gz, the output is set00_corr.nii.gz
Input is the 4D data.
>
> (V) Use BET to create binary mask. The input file is set00_corr.nii.gz
input is the b0 3D data.
>
> (VI) Use DTIFIT Reconstruct diffusion tensors to create FA image.  The
> input file is set00_corr.nii.gz.
input is the 4D eddy corrected data
>
> Now I get dti_FA.nii.gz file.  Is this file have the FA values?

yep.  i would suggest that you check the color map, to make sure your
bvecs are correctly applied.  you can go to fsl website to get a template
of color coded FA image.

>
> If I want to do ROI analysis, how can I extract the FA values after
> the ROI is defined, which FSL should I use?

I do not know this part.  please teach me if you know the answer later.

>
> Your comments are highly appreciated.
>
> Jiansong
>


Sheu, Yi-Shin
Research Assistant
McLean Hospital
Developmental Biopsychiatry Research Program
Tel: 617-855-2942
Fax: 617-855-3712
email: [log in to unmask]