Hi - just to follow up on Andreas, you can do this by simply changeing the
header (of data) to reflect the true number of slices and volumes - the
rest of the conversion is probably fine.
To change the header file, use avwedithd or avwcreatehd (to write a new
one!)
T
On Thu, 15 Sep 2005, Andreas Bartsch wrote:
> Hi,
>
> your data file is not correct: You need to input a 4D-file, yours is only 3D. Furthermore, its 3rd dimension should equal your number of slices, i.e. 20 and not 260.
> So if you fix your data conversion you may be fine.
> Cheers-
> Andreas
>
>
> -----Ursprüngliche Nachricht-----
> Von: FSL - FMRIB's Software Library im Auftrag von Jenifer Juranek
> Gesendet: Do 15.09.2005 00:41
> An: [log in to unmask]
> Betreff: [FSL] bedpost_datacheck ->mismatch error
>
> Hi,
> I'm experiencing "user error" with my attempts to use DTIFit to analyze
> 12MDDW data acquired on a 3T Siemens Trio. I have attempted to follow the
> advice in the email archive re: bvals and bvecs, but have been unsuccessful
> in generating files using DTIFit to Reconstruct diffusion tensors with my
> data (attempts using posted data from the FSL course have been successful).
>
> I get errors when I run bedpost_datacheck on my data, specifically "the
> number of elements in bvals and bvecs are not equal to the number of vols in
> data". I have 260 images total, 20 slices/direction, and I have 13
> directions (b=0 x1; b=1000 x12). The bvecs were obtained from Siemens. The
> output of bedpost_datacheck is appended below:
>
> TIA for suggestions to correct "user error",
>
> Jenifer
>
> $more output.txt
> ./data
> dim1 128
> dim2 128
> dim3 260
> dim4 1
> datatype 4
> pixdim1 1.5625
> pixdim2 1.5625
> pixdim3 6.545
> pixdim4 0.0000
> cal_max 255.000
> cal_min 0.000
> glmax 255
> glmin 0
> origin1 0
> origin2 0
> origin3 0
> file_type NIFTI-1+
>
> ./nodif
> dim1 128
> dim2 128
> dim3 260
> dim4 1
> datatype 4
> pixdim1 1.5625
> pixdim2 1.5625
> pixdim3 6.545
> pixdim4 0.0000
> cal_max 255.000
> cal_min 0.000
> glmax 255
> glmin 0
> origin1 0
> origin2 0
> origin3 0
> file_type ANALYZE-7.5
>
> ./nodif_brain_mask
> dim1 128
> dim2 128
> dim3 260
> dim4 1
> datatype 4
> pixdim1 1.5625
> pixdim2 1.5625
> pixdim3 6.545
> pixdim4 1.0000
> cal_max 1.000
> cal_min 0.000
> file_type NIFTI-1+
>
> num lines in ./bvals
> 1
> num words in ./bvals
> 13
> num lines in ./bvecs
> 3
> num words in ./bvecs
> 39
> number of elements in bvals is not equal to number of vols in data
> number of elements per line in bvecs is not equal to number of vols in data
>
--
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
-------------------------------------------------------------------------------
|