Hi Tommaso,
you need to remove any extensions from the bvals and bvecs files. If you use Textedit, for example, the files will be saved as .rtf. You need ASCII format, so you 'd better use emacs and make sure that you save the files as "bvals" and "bvecs".
By the way, I can see that you only have 7 DW volumes? You cannot perform probabilistic tractography with 2 fibres per voxel at this low number of diffusion directions. Also, you ideally want isotropic voxels, is there any reason you have so thick slices?
Cheers,
Stam
On 5 Jul 2010, at 13:55, Tommaso Gili wrote:
> Hi everyone,
>
> I can't overcome my problems with bedpostx. I am using FSL 4.1.5, on a Mac
> OSX Tiger (10.4.11) and all the files seems to be in right format, but
> when I run bedpostx it declares that there are not bvecs and bvals files.
> I tried with bepostx_datacheck and this is the result:
>
>
> /Users/TG/Desktop/prova/bedpostx/data
> data_type INT16
> dim1 128
> dim2 128
> dim3 40
> dim4 7
> datatype 4
> pixdim1 1.7968750000
> pixdim2 1.7968750000
> pixdim3 4.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> /Users/TG/Desktop/prova/bedpostx/nodif_brain_mask
> data_type INT16
> dim1 128
> dim2 128
> dim3 40
> dim4 1
> datatype 4
> pixdim1 1.7968750000
> pixdim2 1.7968750000
> pixdim3 4.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> num lines in /Users/TG/Desktop/prova/bedpostx/bvals
> cat: /Users/TG/Desktop/prova/bedpostx/bvals: No such file or directory
> 0
> num words in /Users/TG/Desktop/prova/bedpostx/bvals
> cat: /Users/TG/Desktop/prova/bedpostx/bvals: No such file or directory
> 0
> num lines in /Users/TG/Desktop/prova/bedpostx/bvecs
> cat: /Users/TG/Desktop/prova/bedpostx/bvecs: No such file or directory
> 0
> num words in /Users/TG/Desktop/prova/bedpostx/bvecs
> cat: /Users/TG/Desktop/prova/bedpostx/bvecs: No such file or directory
> 0
> cat: /Users/TG/Desktop/prova/bedpostx/bvals: No such file or directory
> cat: /Users/TG/Desktop/prova/bedpostx/bvals: No such file or directory
> Runtime error (func=(main), adr=3): Divide by zero
> cat: /Users/TG/Desktop/prova/bedpostx/bvecs: No such file or directory
> cat: /Users/TG/Desktop/prova/bedpostx/bvecs: No such file or directory
> Runtime error (func=(main), adr=3): Divide by zero
> /usr/local/fsl/bin/bedpostx_datacheck: line 51: [: too many arguments
> /usr/local/fsl/bin/bedpostx_datacheck: line 55: [: too many arguments
> /usr/local/fsl/bin/bedpostx_datacheck: line 59: [: too many arguments
> number of elements in bvals is not equal to number of vols in data
> /usr/local/fsl/bin/bedpostx_datacheck: line 67: [: too many arguments
>
>
> Any idea?
> I saved bvecs and bvals using emacs and textedit, but the result has been
> the same.
>
> Thanks
>
> Tommaso
>
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