From a06cf3ab49f737c8a73bfd62b4dcbe596204ea7d Mon Sep 17 00:00:00 2001 From: Paul Yushkevich Date: Thu, 5 Dec 2024 14:45:09 -0500 Subject: [PATCH] Documentation update with T2 example --- README.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/README.md b/README.md index e959644..11c7eb5 100644 --- a/README.md +++ b/README.md @@ -102,6 +102,28 @@ python3 -m crashs fit \ You should find the output from running CRASHS in folder `/my/crashs/folder/sample_data/ashs_pmc_t1/subj01/crashs`. +### T2 Example + +Another example in the `sample_data` folder can be used to test CRASHS for T2-weighted MRI processed with the ASHS-PMC atlas. It is better to run this example on a machine with an NVidia GPU because a nnU-Net is used by CRASHS to generate the white matter label; otherwise expect it to take 30-60 minutes to complete. If using Docker, include the flag `--gpus all` when calling the `docker run` command to make the GPU available to the container. + +You can run the example in the Docker container like this: + +```sh +python3 -m crashs fit -C /package -s left -c heur \ + /data/ashs_pmc_alveus/subj02/ashs \ + ashs_pmc_alveus \ + /data/ashs_pmc_alveus/subj02/crashs +``` + +Or using CRASHS pip install like this: + +```sh +python3 -m crashs fit -s left -c heur \ + /my/crashs/folder/sample_data/ashs_pmc_alveus/subj02/ashs \ + ashs_pmc_alveus \ + /my/crashs/folder/sample_data/ashs_pmc_alveus/subj02/crashs +``` + ## Outputs from CRASHS The program generates many outputs, but the most useful ones are: * `fitting/[ID]_fitted_omt_hw_target.vtk`: the grey/white and grey/csf boundaries estimated by the `cruise_cortex_extraction` module of NighRes. These meshes are in physical (RAS) coordinate space, not in voxel (IJK) space output by Nighres. *If you extract meshes from the T1-ASHS segmentation in ITK-SNAP, those should line up with these meshes.*