Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination

Submissions for the Tractostorm 2 Project [1]  from our collaborators (raters) are available for new analysis.
Contains regions of interest (ROIs) as well as resulting bundles. Segmentations were performed with MI-Brain [2] (MI-Brain)

Initial data is the same as in the initial Tractostorm Project [3]
Contains the data as sent to collaborators and the written document containing the dissection protocol in detail.

[1] Rheault, Francois, et al. "Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination." Human Brain Mapping (2022).
[2] Rheault, Francois, et al. "MI-Brain, a software to handle tractograms and perform interactive virtual dissection." Proceedings of the ISMRM Diffusion study group workshop, Lisbon. 2016.
[3] Rheault, Francois, et al. "Tractostorm: The what, why, and how of tractography dissection reproducibility." Human brain mapping 41.7 (2020): 1859-1874.

Data Organization:
The 5 HCP subjects were duplicated 4 times each.
193441 -> A111, B218, C317, D418
219231 -> A127, B228, C320, D426
286650 -> A136, B237, C338, D436
486759 -> A149, B246, C344, D443
615441 -> A156, B252, C359, D450

Bundles can be segmented automatically using the scilpy toolbox.
scil_filter_tractogram.py ${INPUT} ${OUTPUT} ${OPTIONS}

${INPUT} would be the whole brain tractogram of an HCP subject in data_to_segment.zip

${OUTPUT} would be the bundle filename (preferably .trk format)

${OPTIONS} would be the sequence of ROIs to apply, one for each bundle.

CC: '--drawn_roi CENTRAL_CC.nii.gz any include --drawn_roi LOWER_AXIAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude --drawn_roi POST_C_R.nii.gz any exclude --drawn_roi PRE_C_R.nii.gz any exclude'

AF_L: '--drawn_roi CENTRAL_CS_L.nii.gz any include --drawn_roi MEDIAL_SAGITTAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any include --drawn_roi PRE_C_L.nii.gz any include --drawn_roi TEMPORAL_ENTRY.nii.gz any include --drawn_roi TEMPORAL_STEM.nii.gz any exclude'

PYT_L: '--drawn_roi IC_L.nii.gz any include --drawn_roi MO_L.nii.gz any include --drawn_roi MB_L.nii.gz any include --drawn_roi MO_L_NOT.nii.gz any exclude --drawn_roi MID_SAGITTAL_PLANE.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude'