Closed shen4brains closed 3 years ago
Also poor brain extractions in dMRI data (see pptx in Slack); relevant dMRI extractions occur here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/35483bfcafb52db9a510afd18bada12203653c78/bb_diffusion_pipeline/bb_eddy/bb_pre_eddy#L46
dMRI brain extraction issue may be specific to camCAN; as of yet haven't seen this consistently in ADNI
T1 brain extraction is sometimes poor in ADNI3
Original issue not due to poor brain extractions but to the earlier failure of nonlinear registrations; Opened new issue #76 to address nonlinear registrations. Keeping this issue open as it still applies to ADNI3 T1 data, and maybe camCAN dMRI data as well
Final decision re: 1) ADNI3 T1 brain extractions: not improved by optiBET (cf @shen4brains' local branch add_optiBET) so T1 brain extractions will remain as-is 2) cam-CAN dMRI B0 brain extractions improved by adopting T1-style brain extractions (applying MNI_brain via warp to native space) and implemented across all branches (master, cam-CAN, ADNI3) for consistency
Pipeline currently relies on BET for brain extractions; may need alternative brain extraction techniques to achieve better performance in older adult data. Example subjects with poor brain extractions in camCAN dataset include: sub-CC120987, sub-CC420241, sub-CC512003, sub-CC720497 and sub-CC723395
Relevant code here: https://github.com/McIntosh-Lab-RRI/tvb-ukbb/blob/35483bfcafb52db9a510afd18bada12203653c78/bb_structural_pipeline/bb_struct_init#L46-L47