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Hi Saad,

Thanks for talking a look! Line 59 is modified from the original script. It
basically allowed you to run the script from outside the directory by
splitting the string at the "/". Thats how I had my scripts set up..

For example: rotate_bvecs2 testdir/test.ecclog testdir/test.bvec;


To do it within a directory, line 59 does need to be altered to:
matfile=$(remove_ext $(echo ${line} | grep processing | awk '{print $2}'));

For example: rotate_bvecs2 test.ecclog test.bvec;


I have a attached a zip file with:

1. the corrected rotate_bvecs2 script
2. a text file with sample output (what the terminal prints when all goes
well), as well as the command syntax
3. a working bvec file
4. a working ecclog file
5. my corrected "test_rot.bvec" file

Please let me know if this works on your end. Thanks for catching this
error!


Best,

Dave Deriso


On Thu, Mar 11, 2010 at 1:48 AM, Saad Jbabdi <[log in to unmask]> wrote:

> Hi Dave,
> Thanks for your suggestions.
> I agree with you that it is best to name the output <blah>_rot
> However, your script does not work - in particular I am wondering about
> line 59 - what is that for? That line is causing the script to fail from my
> side.
>
> So I will make the relevant changes re the ouput name, but will keep the
> rest as it is...
>
> Cheers, and thanks again.
> Saad
>
>
> On 9 Mar 2010, at 08:54, Dave Deriso wrote:
>
> Hello,
>
> I'm new here. My name is Dave Deriso and I am an undergrad researcher at
> UCSD Psychiatry/Psychology under Dr. Martin Paulus and Dr. Ramachandran. I
> was following the DTI pipeline on the FSL site and everything was going well
> until I tried to run rotate_bvecs. For some reason, it just wouldn't work. I
> doubt my OS has anything to do with it, but I am using a mac air laptop
> running OSX Snow Leopard (10.6.2).
>
> Anyway, I decided to go ahead and rewrite the problematic portions. The new
> script (attached) runs without problems. In addition, I added:
>
>  - safety measure: make sure you are running an ecclog file instead of the
> ecc nifti.
> - changed the output to "myBvec*_rot.*bvec", this basically adds a "_rot"
> to your existing file name. The original version simply made a backup copy
> of your original bvec file, and named it bvec.bvec_old. bvec_rot is better
> because it indicates that this file has been transformed..
>
> Please have a look and make sure I didn't make an error somewhere!
>
> Best,
>
> Dave Deriso
> UCSD Psychiatry
> <rotate_bvecs2>
>
>
>    --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466  (fax 717)
> www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad>
>
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