Hi Joe
As you suggested, can you please check that the data files are OK and consistent between the two subjects? The fact that you followed the same process does not guarantee that things cannot go wrong. A second thing that I would check is the brain mask, make sure that for the problematic dataset you have a well-defined binary brain mask.
Cheers
Stam
On 22 Jan 2016, at 14:39, Joe Harding <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I am having trouble running the bedpostX process on some of my diffusion data. It worked fine for the first patient, taking several hours to analyse the 69 slices and produce the outputs listed in the FDTwiki. However when I tried to rerun the process for another couple of patients (individually), it finished in 30 seconds and hasn't produced all the outputs. The script says:
>
> "Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> 0 slices processed
> Queuing post processing stage
> Done!"
>
> This is different to the first patient where the script listed the each of the 69 slices that have been processed, whereas here it only listed "0 slices processed". I have run a data check on the directories of one of the two patients that haven't worked and the script says:
>
> "bedpostx_datacheck ./
>
> num lines in .//bvals
> 1
> num words in .//bvals
> 33
> num lines in .//bvecs
> 3
> num words in .//bvecs
> 99
> number of elements in bvals is not equal to number of vols in data
> number of vectors in bvecs is not equal to number of vols in data"
>
> I also ran a data check on the successful directory:
>
> "bedpostx_datacheck ./
>
> num lines in .//bvals
> 1
> num words in .//bvals
> 33
> num lines in .//bvecs
> 3
> num words in .//bvecs
> 99"
>
> As you can see, the number of words and lines in the bvec and bval files of the two patients are the same. That leads me to think that there are different numbers of slices in the data.nii.gz files of the two patients. However I can't think of why there would be this difference between these files. I have run the same processes on all of the patients (DICOM to nifti conversion and eddy current correction).
>
> Can you see what the problem is?
>
> Kind regards,
>
> Joe
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