Dear Mark


This is great news!


Thanks for your help,



From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
Sent: 19 April 2013 17:19
To: [log in to unmask]
Subject: Re: [FSL] fdt_rotate_bvecs


Hi Zita,


I assume you are running on an Ubuntu/Debian system.

If so, try changing the first line of the script to:




instead of:




Oh, and the script is now official, as of FSL 5.0.2.  :)


All the best,




On 19 Apr 2013, at 16:40, "Patai, Zita" <[log in to unmask]> wrote:

Dear FSL


I realize that this script is not ‘official’, but since it exists I was trying to use it as I have 3 acquisitions per subject.


I am using it as: fdt_rotate_bvecs original_bvecs output ecc_logfile


and get this error (I am only showing the last bit, but this exists for all images in the series, which is 63):


/usr/share/fsl/5.0/bin/fdt_rotate_bvecs: 29: [: processing dti_ec_tmp0062: unexpected operator

/usr/share/fsl/5.0/bin/fdt_rotate_bvecs: 67: /usr/share/fsl/5.0/bin/fdt_rotate_bvecs: let: not found


I can’t seem to get around this error, and I have checked my ecc_logfile and it looks fine. Also, it creates an output file, but it only has 3 zeros in it.


Please let me know if there is a solution!


Many thanks




Eva Zita Patai

Postdoctoral Research Associate

UCL, Institute of Child Health

020 7905 2730