Hello Dear Stamatios,

Thank you so much for your suggestions, I appreciated. I used same way as suggested bvecs and bvals files before on some other data (GE 3 T MRI scanner with 30 diffusion direction) set and it work but now I am start working on DTI data which was acquired on 3 T Siemens skyra MRI scanner with 64 diffusion direction. I am getting this error?
Any suggestions highly appreciated.

Thanks
Manoj

On Fri, Sep 18, 2015 at 8:46 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote:
Hi

Bedpostx requires “bvecs" and “bvals" as filenames. No xxx. It expects these filenames, because it is a wrapper that automatises many options. So a minimum input required from the user is certain name conventions. 

If you’d rather use your own naming conventions, you can call directly the underlying binary (which is xfibres), but you need to figure out all the options yourself and parallelise manually. 

Cheers
Stam



On 18 Sep 2015, at 13:37, Michael Knight <[log in to unmask]> wrote:

bedpost is picky with naming too. I believe it requires xxx.bvecs, not xxx.bvec, even if the format is right! (And dcm2nii gets it right, as others have pointed out)

On 18 September 2015 at 11:03, Vasilis M. Karlaftis <[log in to unmask]> wrote:
Dear Manoj,

I think it will be really helpful if you upload your bvec and bval files that you get from dcm2nii. These are specific for your scanner sequence so no one else can create them for you.
If you can't get your files correctly from the dicom files, the other option I can think of is to contact your scanner facility. They should definitely have a protocol for the sequence used in each scan, from where you can retrieve the gradients and b-values used.

Best regards,
Vasilis

On 18 September 2015 at 10:12, rakesh rakesh <[log in to unmask]> wrote:

Hi Manoj,
Did you try dcm2nii

https://www.nitrc.org/frs/shownotes.php?release_id=1855

https://www.nitrc.org/projects/dcm2nii/

We have been working with Siemens trio 3 Tesla. We are able to get these bval & bvec files using dcm2nii

All the best.

On Sep 18, 2015 2:40 AM, "Manoj Kumar" <[log in to unmask]> wrote:
Hello Dear FSL experts,

I will really appreciate your help, if someone can provide me bvecs and bvals files for 3 T Siemens Scanner. We have acquired 64 dir DTI data using b=2000.
I need these file to run the BEDPSOT steps in FSL. I did generate the bvecs and bvals file from original DICOM DTI data using MRIcro but it does not work. I also try to rearrange these bvecs abd bvals file several different ways and rerun the BEDPSOT but none of these work.
I am getting message (abnormal signal.........child killed) when I run the Bedpost in FSL.

Thanks in advance for all your help.

Best
Manoj