macapype
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Macatools
PNH segmentation pipelines based on nipype
Hi, thanks for making this package! I successfully installed macapype via Docker and tried to run it using the instructions provided [here](https://macatools.github.io/macapype/docker_install.html). Unfortunately, `/opt/packages/macapype/workflows/` used in the commands does not...
Inspired from subject `sub-032159` in `site-mountsinai-S` from PRIME-DE, which fail miserably since the first step of macapype. Here is for instance the image after the first stage: - **option 1**...
Even better = all nodes can be params/indiv_params (requires a full wrap) and provide the json all available options
@kepkeeloh suggests to check how the T2w after debiased works instead of the T1w
Sometimes, the T2-weighted images might give better contrast for the WM/GM segmentation, i.e. for very young and poorly myelinated brains. So it would be interesting to adapt macapype to have...
Rather than implementing 3drefit -deoblique on the native image, to implement 3dWarp -card2oblique to convert the transformed template masks (non-oblique) with the same oblique form as the native image.
Re: our Jan 21 meeting here are two examples of the atlas brex documentation. I think the piece that is missing is a listing of the actual params, and roughly...
-IsoSurface (AFNI) is bugging as libXp6.so is missing, fixed in skullTo3d but would make more sense to add it in the macapype_env directly - the clean up is not properly...