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
Hi Dave,Thanks for your suggestions.I agree with you that it is best to name the output <blah>_rotHowever, 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.SaadOn 9 Mar 2010, at 08:54, Dave Deriso wrote:<rotate_bvecs2>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
--Saad JbabdiUniversity of Oxford, FMRIB CentreJR Hospital, Headington, OX3 9DU, UK(+44)1865-222466 (fax 717)