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
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?
(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.
(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?
(IV) Use FDT to do Eddy current correction. The input file is
set00_data.nii.gz, the output is set00_corr.nii.gz
(V) Use BET to create binary mask. The input file is set00_corr.nii.gz
(VI) Use DTIFIT Reconstruct diffusion tensors to create FA image. The
input file is set00_corr.nii.gz.
Now I get dti_FA.nii.gz file. Is this file have the FA values?
If I want to do ROI analysis, how can I extract the FA values after
the ROI is defined, which FSL should I use?
Your comments are highly appreciated.
Jiansong
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