Dear developers
I ran the minimal preprocessing pipeline on a number of my own subjects,
and recently noticed that there was a rather unfortunate AP flip of the EPI
during registration for ~30% of the subjects (explaining some rather odd
results that I have been trying to track down for a couple of days).
The first volume in which I can notice this AP flip is the
"Scout_gdc_undistorted_fieldmap2str.nii.gz" in
"${SUBJECT_DIR}/${RUN}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/"
(that the first first showing the incorrect AP orientation, according to
`ls -lat`) . I'm having a hard time tracking down in the code
(DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh) where
this volume is created/used, and hence how to remedy the bug.
Let me know if you can help. Thanks!
- Julien
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