Dear all,
I want to weigh in here: the current default behavior of the pipeline is
not doing a good job at motion correction (in my own data).
First a quick digression:
The code in global/mcflirt_acc.sh indicates that you are taking the 10th
volume as a reference, in the absence of a supplied reference:
line 29:
${FSLDIR}/bin/fslroi $input ${output}_ref 10 10
I think that maybe you meant to take the average of the first 10 volumes
(as Greg B. indicated, and given the following lines of code); so line 29
should likely be changed into:
${FSLDIR}/bin/fslroi $input ${output}_ref 0 10
But I don't think this is where the issue comes from. Indeed, running
mcflirt with the 10th volume gives a fine result. There is thus something
else in mcflirt_acc that is not functioning properly (at least for data
other than HCP), compared to the standard FSL's mcflirt.
Can you give the rationale for writing your own mcflirt function
(mcflirt_acc.sh), and explain how it differs from FSL's mcflirt? (I could
also go compare with the source code for mcflirt, but I thought I would ask
directly since you probably had a good reason)
Thanks!
- Julien
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