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add plan for synthSR #2

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add plan for synthSR #2

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@leej3 leej3 commented Sep 16, 2025

A quick sanity check on the next step... let me know if you have any suggestions. Will have this run by next week.

@leej3 leej3 requested a review from Shotgunosine September 16, 2025 15:56
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leej3 commented Sep 19, 2025

Some thoughts:

  1. recon-all doesn't have synthSR output, just synthseg
  2. recon-any only has synthSR.mgz: it's skullstripped and as far as I can tell intensity normalized and contrast enhanced. My understanding is that it needs to be combined with -noskullstrip -xmask <brainmask.mgz> to work.
  3. recon-all clinical has synthSR.raw.mgz that can be run through the full pipeline with less deviation.

@leej3
adjust plan
3a1e103 
only run raw synthsr output from the RAC pipeline
fix bugs in functions/notebook
make sure nbstripout filter works
@leej3
add recon-all 8.1
37c81aa
@leej3
adjust fs processing
7c7e220
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