Hi Saad,

Thank you for your prompt reply. I am actually using the GUI from FSL 4.1.6. where when I check the option of reorienting the bvecs it asks me to specify a nifti file.

Should I move this script into the bin directory? If yes, I will need to ask the IT people to do it since I do not have permissions to that directory.

Also, will this script work through the GUI for correcting the bvecs?

Thanks and kind regards,
Shail

On 18 April 2012 13:57, Saad Jbabdi <[log in to unmask]> wrote:

It shouldn't ask for a nifti file.

Which script are you using? Please use the one attached.

Saad

 

On 18 Apr 2012, at 12:30, Shail Segobin wrote:

Dear experts,

I am very new to DTI and trying the processing steps for the very first time.

In the Eddy current correction step, I would like to know why the reorient bvecs wants a nifti image instead of transformation parameters and if anyone could please tell me where to get this file from?

I have sifted through questions on the mailing list and did not really get a concrete answer to this question.

Many thanks for your time and help

Shail

--

Saad Jbabdi

University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK

(+44)1865-222466  (fax 717)

www.fmrib.ox.ac.uk/~saad