If you have a bunch of files with suffixes that Bestpostx doesn’t recognize, you can leave them untouched but create symlinks to them with the correct names.

For instance if you have a file called abc.xyz which requires “bvecs” as a suffix, you can do:   ln –s abc.xyz abc.bvecs

Best regards,

Don

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stamatios Sotiropoulos
Sent: Friday, September 18, 2015 8:47 AM
To: [log in to unmask]
Subject: Re: [FSL] Gradient table (bvecs and bval) for Siemens 3T

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