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Hi Raphael,
 
just a few quick checks:
 
- Are bvecs and bvals consistent with each other? The first zero entries in the bvals do not correspond to zero entries in the bvecs.
- Could you replace commas with dots in the bvecs file and retry?
 
Cheers,
Stam
----- Original Message -----
From: [log in to unmask] href="mailto:[log in to unmask]">Raphael Hilgenstock
To: [log in to unmask] href="mailto:[log in to unmask]">[log in to unmask]
Sent: Tuesday, September 21, 2010 6:58 PM
Subject: [FSL] dtifit - all white FA image

Dear FSL-Experts,

after running dtifit without any error message my FA-map is all white. This has been discussed on the list before but I think that I`ve got a different problem than the one(S) discussed earlier.

To avoid the most common errors I

1.) used the "dos2unix" command to remove carriages returns added by evil Windows and checked the output using the "cat -v" argument.

2.) made sure that my bvals and bvecs also comprise the no-diffusion data (in a column-wise fashion) and that the files are without any extension (e.g. txt)

3.) checked that the bvec-file is showing no repetitions of gradietens

4.) run the Diffusion-Toolkit in combination with Trackvis to make sure that the gradient scheme gives reasonable results (and is does)

6.) took a look at the "eddy current" output and my brain mask that look fine

7.) checked my data with bedpostx_datacheck which gave me the following results:

/home/stendal/rhilgens/X/data.../data
data_type      INT16
dim1           110
dim2           110
dim3           64
dim4           76
datatype       4
pixdim1        2.2000000477
pixdim2        2.2000000477
pixdim3        2.2000000477
pixdim4        1.0000000000
cal_max        0.0000
cal_min        0.0000
file_type      NIFTI-1+

/home/stendal/.../nodif_brain_mask
data_type      FLOAT32
dim1           110
dim2           110
dim3           64
dim4           1
datatype       16
pixdim1        2.2000000477
pixdim2        2.2000000477
pixdim3        2.2000000477
pixdim4        1.0000000000
cal_max        0.0000
cal_min        0.0000
file_type      NIFTI-1+

 num lines in /home/fsl/Desktop/MM_T2//bvals
1
 num words in /home/fsl/Desktop/MM_T2//bvals
76
 num lines in /home/fsl/Desktop/MM_T2//bvecs
3
 num words in /home/fsl/Desktop/MM_T2//bvecs
228

And still my FA-map is all white with a value of 1. I`m a little lost (and desperate) here and would appreciate any help on this. As the bvecs and bvals-files are small I attached them.

Thanks in advance and best regards
Raphael H.

___________________________________________
Dipl.-Psych., cand.med. Raphael Hilgenstock
Klinik für Neurologie
Erlanger Allee 101
07747 Jena

Tel: +49 3641 543514