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simplified use of manual segmetation (#325)
* removed segT*w * cropseg to manualseg * Port v1.5.2 bugfixes into dev-v2.0.0 (#329) (#331) * fix for using T1T2w model run_inference was only accepting a single input image, this makes it accept a list of images too, and makes it so --force-nnunet-model T1T2w grabs both T1w and T2w as inputs. * hipp curvature was being used always, instead of wildcard this didn't affect any workflow computations, just the subsequent dscalar.nii and spec file that would have the wrong curvature map * fix logical error * Bump version to 1.5.2-pre.1 * Bump version to 1.5.2-pre.2 * keep pipeline_description changes --------- Co-authored-by: Ali Khan <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * minor bugfix for passing modality * lint * cleaned more instances of segTxw * lint * removed unneeded def --------- Co-authored-by: Jordan DeKraker <[email protected]> Co-authored-by: Ali Khan <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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index name abbreviation | ||
1 hippocampal grey matter GM | ||
2 SRLM or 'dark band' SRLM | ||
3 neocortex (entorhinal or parahippocampal) MTLC | ||
4 pial surface Pial | ||
5 hippocampal-amygdalar transition area HATA | ||
6 indusium griseum IndGris | ||
7 cysts Cyst | ||
8 dentate gyrus DG |
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#No. Label R G B A | ||
1 subiculum 41 43 252 0 | ||
2 CA1 102 209 216 0 | ||
3 CA2 0 179 60 0 | ||
4 CA3 255 182 0 0 | ||
5 CA4 255 43 23 0 | ||
6 dentate_gyrus 245 236 0 0 | ||
7 SRLM 119 54 155 0 | ||
8 cysts 255 255 255 0 |
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