Hi MRtrix3 team, @ThijsDhollander @jdtournier
I am investigating reproducible dwi2response dhollander failures in a small number of subjects. After inspecting the retained temporary files, I now seem to have two related failure patterns.
For two subjects, the crude CSF pool is large (~13–14k voxels) (e.g attached CASE 1), but CSF refinement collapses it to only 1–2 voxels. The subsequent CSF response-voxel selection then fails because 10% of the refined pool rounds to zero.
For another subject (attached CASE2), the problem occurs earlier. The safe_mask contains 402,936 voxels and is partitioned as:
crude WM: 193,182
crude GM: 209,752
crude CSF: 2
The FA image and DWI volumes look visually okay. The two voxels classified as crude CSF have very high SDM values (one around 7), while essentially the entire remaining non-WM pool is classified as crude GM.
From reading the Dhollander implementation, my understanding is that automatic mrthreshold operations are used both when splitting the low-FA/non-WM pool into crude GM versus crude CSF and later during CSF refinement.
It seems that very small number of extreme SDM values can cause the automatic threshold to isolate only the extreme tail, resulting in biologically implausibly small CSF pools even when the underlying DWI and FA images appear otherwise reasonable
I would be very interested in your thoughts on:
. Is this behaviour an expected failure mode of the current Dhollander algorithm?
. Is it correct that a handful of extreme SDM values dominate the automatic mrthreshold split in either the crude GM/CSF separation or the later CSF refinement?
. Is there any built-in safeguard intended to prevent a tissue candidate pool from collapsing to only one or a few voxels?
. If the extreme-SDM voxels can be shown spatially to be implausible and/or associated with abnormal underlying DWI signal, would excluding those voxels from the response-estimation mask and rerunning otherwise standard Dhollander be a reasonable approach?
. Would it make sense for Dhollander to flag an extreme crude→refined or non-WM→CSF collapse before proceeding to response-voxel selection?
I attached, SDM histograms before and after the relevant splits, crude/refined tissue counts, spatial locations of the extreme-SDM voxels, and their underlying per-volume DWI signal.
Please your response
BW
William
dwi2response.pdf (3.4 MB)