Hello FSL experts,
I am trying to run dtifit on my data, and it runs through with no errors, but when I open the FA map, it looks like it just returned my brain mask. I have seen that others have run into this problem before, but none of the solutions for them seem to be working here.
Our acquisition is a little old, and includes getting to two identical DTI acquisitions with one b0 and 30 directions each. These scans were concatenated and run through eddy. The bvals and bvecs files were also concatenated (in the same order), in a 3x62 matrix, with the 0s corresponding to the b0s in the data (the last volume of each scan). I have made sure these files end with the appropriate carriage, I have checked my output data from eddy as well as the brain mask and both look normal, and running the data through bedpostx_datacheck returns the following:
bedpost/data
data_type FLOAT32
dim1 256
dim2 256
dim3 60
dim4 62
datatype 16
pixdim1 0.828000
pixdim2 0.828000
pixdim3 2.200000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
bedpost/nodif_brain_mask
data_type INT16
dim1 256
dim2 256
dim3 60
dim4 1
datatype 4
pixdim1 0.828000
pixdim2 0.828000
pixdim3 2.200000
pixdim4 1.000000
cal_max 1.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in bedpost/bvals
1
num words in bedpost/bvals
62
num lines in bedpost/bvecs
3
num words in bedpost/bvecs
186
I am wondering if using two scans with the same acquisition is introducing this issue? Otherwise my money is on an error being in the bvecs file, however after running through eddy successfully I don't know what. Any help is much appreciated!
Josh Robinson
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