AFNI Message Board

History of AFNI updates  

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March 12, 2021 09:08AM
Hi, Pawel-

There are a couple things here:
First, we do keep histories of changes, both in this history text file, gateway'ed here:
[afni.nimh.nih.gov]
and in the github:
[github.com]
The second is more finegrained, because every bit of change is recorded in detail.

I note that AFNI binary version 21.0.08 got built on Feb 11, 2021, and ver 12.0.13 got built on March 3, 2021.


Second, with afni_proc.py (AP), gen_ss*review*.py and TSNR---
AP used to apply a mask to the TSNR dset, but now it no longer does that, so we can see it every TSNR everywhere in the brain. You should also get QC images of TSNR now in the APQC HTML.


Third, with skullstripping/processing:
Something that could throw skullstripping off, esp. if you have subj from a different session, is the coordinates not being good. That is, if (x,y,z)=(0,0,0) is not loosely central in the volume/dset, then 3dSkullStrip might fail about growing a surface outward (how it works). So, that is something to check for this subject where it fails. It also sounds like you are changing a script between these tests, and could that be introducing a change?

I don't see any major changes to 3dSkullStrip in that interval. There was a change with NIFTI I/O, but that was something that applied in some very particular case(s).
A test of changes/failure would be if: you have one script+AFNI Binary version that worked today on a particular dataset, and then if, on the very same dataset and using the same script, processing failed with an updated binary version. Very small changes in a script miiight affect things--e.g., the coordinates.

If you have a dataset and a specific command(s) that used to work, but now doesn't, I'd be happy to take a look. Otherwise, with possible script changes and differing datasets, it is a bit hard to try to suggest anything.

--pt
Subject Author Posted

3dSkullStrip failure on current but not previous version

Pawel March 11, 2021 11:07PM

Re: 3dSkullStrip failure on current but not previous version

ptaylor March 12, 2021 09:08AM

Re: 3dSkullStrip failure on current but not previous version

Pawel March 12, 2021 09:47AM

Re: 3dSkullStrip failure on current but not previous version

ptaylor March 12, 2021 10:54AM

Re: 3dSkullStrip failure on current but not previous version

ptaylor March 16, 2021 07:12PM

Re: 3dSkullStrip failure on current but not previous version

Pawel March 16, 2021 10:33PM



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