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I'd like to add picking to source spaces, vertices and connectivity.
Instead of passing full fsaverage group matrices with spatial excludes it would be much more memory saving to only pass a supset of…
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recon all run from init_subj seems to make the fiducial surface files lh and rh.fiducial in the freesurfer surfs directory
make_fiducial also runs without error but I'm not sure if it does anything
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The rules for which files go in "anatomicals" vs. "surface" vs. "cache" seem arbitrary. Especially the distinction between "cache" and "anatomicals", both of which contain items that are generated on-…
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I need to propagate surface labels through cortical volumes, but because mindboggle now combines ants and freesurfer segmentations and will soon accept modifications to surface labels, I don't have se…
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I'm experimenting with reprozip as a way to package up software stacks for version quarantine, so I ran it against a test set of data and now I'm trying to pack up the experiment, here's my config fi…
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i put mindboggle turtle terms in a wiki, but all of the indentation disappeared, so i am including mbterms.ttl here. in addition to some basic terms at the beginning, i include all of the (cortical) …
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My colleague Mohammad and I found that we get a better segmentation (and thickness measure) by combining FreeSurfer (FS) and ANTs (Atropos) outputs (see below and the new functions combine_whites_over…
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and parts of it running only for wm mask correction / inspection:
it is at the end of the step2 that you need to check and corrected if needed the wm.mgz (white matter volume) and and relaunched the …