Yi-Shin:
Thanks a lot.
Jiansong
On Jan 18, 2008, at 11:19 AM, Sheu, Yi-Shin wrote:
>> 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]
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