TractX: whole-brain tracking and SIFT run

SIFT COMPLETE — 20 million → 2 million
keep FOD + mask + both tractograms together. SIFT filtering and SIFT2 weights are different outputs, don't mix filenames

files: the command operates in the template directory. Keep FOD.mif, template_mask.mif, the unfiltered tractogram and SIFT output linked in the run record. stream_gen.py is the corresponding flowchart script.

recorded state: “SIFT COMPLETE.” The journal gives this command sequence:

tckgen -angle 22.5 -maxlen 250 -minlen 10 -power 1.0 FOD.mif \
  -seed_image template_mask.mif -mask template_mask.mif \
  -select 20000000 -cutoff 0.06 tracks_20_million.tck
tcksift tracks_20_million.tck FOD.mif tracks_2_million_sift.tck \
  -term_number 2000000

review questions: verify the image/streamline coordinate space and actual tool version before rerunning. The later bottleneck code also calls tcksift2 to generate weights; do not treat SIFT downsampling and SIFT2 weighting as the same saved artifact. Completion of this stage does not establish successful bundle segmentation or bottleneck resolution.

Whole-brain streamline rendering.
Whole-brain streamline rendering.

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