Bug fix rotate bvec #543
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Bug fix rotate bvec #543
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… without fieldmap files - Added use_fieldmap flag to create_dmri_preprocessing
…put rotated_bvecs file and offsetting the correction by one volume. Noted that the first two entries in the rotated_bvec files were 0,0,0 when the bvalues of the first two files were 0 and 1000. Plotting the original bvec against the rotated bvec (X component) showed what appeared to be a single volume offset (see black and red traces in attached plot) code issue: _rotate_bvec code initialised its output bvec array with the first entry of the input bvec array and then looped through FLIRT matrices starting at 1st position, but used a 0-based index for selecting the input from the bvec array solution : initialise output array filled with zeros, loop through FLIRT matrices from 0, use 0-based indexing for selecting input from the bvec array, set consecutive elements appropriately testing : nothing, other than plotting the X component for one subject
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noted issues: FA files looked funny after processing with this pipeline, the first two entries in the rotated_bvec files were 0,0,0 when the bvalues of the first two files were 0 and 1000.
Plotting the original bvec against the rotated bvec (X component) showed what appeared to be a single volume offset (see black and red traces in attached plot)
code issue: _rotate_bvec code initialised its output bvec array with the first entry of the input bvec array and then looped through FLIRT matrices starting at 1st position, but used a 0-based index for selecting the input from the bvec array
solution : initialise output array filled with zeros, loop through FLIRT matrices from 0, use 0-based indexing for selecting input from the bvec array, set consecutive elements appropriately
testing : nothing, other than plotting the X component for one subject
I attached the plot, where black = original bvec, red = rotated bvec, green = rotated bvec with my solution. The other thing that you can see in this plot is that there are regularly spaced x=0s in both the original and my version where the b=0 volumes were collected (7 in total).
(This also includes the changes that I made in the previous pull request.)
