Hello,
I run into the following error when running rotate_bvecs (FSL 4.1.5):
syntax error near unexpected token `done'
line 21: `done'
first, I did the simple script change in rotate_bvecs script as suggested on this thread:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1001&L=FSL&P=R62549&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
2. FSL4.1.5 has a script that does all that for you. It is called
> rotate_bvecs, and it is based on a donation from Martin Kavec.
> Unfortunately, it has a little bug. If you want to use it you will
> have to edit the text and replace "done" with "fi" at the beginning of
> the script (when it is testing whether it is going to over-write the
> ouput file). Sorry!
After this change, the script run but still have the following error (top missing error message abbreviated..)
....
...
/contrib/projects/fsl/source/fsl//bin/rotate_bvecs: line 48: /tmp/grot23317_/home/wzhou/courses/ENG02912G/HW3/dtiAssignmentData/dtiAssignmentData/DTI_32dir_4b0_b1300_eddyCorrected_tmp0035.mat: No such file or directory
/contrib/projects/fsl/source/fsl//bin/rotate_bvecs: line 50: /tmp/grot23317_/home/wzhou/courses/ENG02912G/HW3/dtiAssignmentData/dtiAssignmentData/DTI_32dir_4b0_b1300_eddyCorrected_tmp0035.mat: No such file or directory
Could not open matrix file /tmp/grot23317_*.mat
Could not open matrix file /tmp/grot23317_*.mat
Could not open matrix file /tmp/grot23317_*.mat
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
the problem is it is not finding the ".mat" file that it needs to do the rotation of bvecs. However, i saw those .mat files being generated WHILE running "eddy_correct", but when "eddy_correct" finish, all those mat file were removed. any clue on how I could fix this problem?
thanks a lot!!
Jin
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