Hi Yuhong,
 
Is it a Philips scanner? If so, the last volunme is ADC volume. For detail you could refer to some Philips document. They use this to do fiber track on scanner.
 
For your bvecs and bvalues, it may due to some txt formate. for example, after you manually deleted the last entry, it may add 0 at the end of file when it is read in FSL/MATLAB. I'm nost sure since I've never tried before. you may want to read the file into MATLAB to check whether something changed.

 
On Fri, Oct 1, 2010 at 9:40 PM, Yuhong Liu <[log in to unmask]> wrote:

Dear FSL experts:

 

I am new fsl users, I have some questions.


I  generated FA image by following the following steps
1: eddy_correct
2: Bet, threshod 0.5
3: dtifit


In the generated FA image,  there are very high intensity in the brain boundary,  and there are some voxels FA > 1, see the attached figure.  The FA image seems to look unclear.


I used DWIs of the 32 directions to generate FA.  I converted decom to .img (.hdr) by MRIConvert.  There are 34 volumes in this 4D image, and I checked bvecs and bvals (see the attached file) and found:
the last gradient direction in bvecs  is 0 0 0, and the last value in bvals is 800,  I am not sure that these files are correct.


But I delete the last volume in 4D image, remove the last gradient direction (0 0 0 ) in bvecs and the last b = 800 in bvals, but I got errors in ditfit:
Errors:  bvecs and bvals don't have the same number of entries.


why? I removed the last gradient direction in bvecs and b value in bvals, respectively.


I saw many old  archives that we can use rotate_bvecs to rotate the bvecs after eddy_correct. Is it necessary? 
I didn't find such command in fsl ( I uses v4.10 version) . If rotate_bvecs is necessary, how should I do?


Any comments,  Thank you in advance


Best


Shugao




--
Xiaowei.Zou

Department of Biomedical Engineering
Columbia University
New York, NY, 10027