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Troubleshooting

You are viewing the documentation for classic ASHS

For new projects we recommend HyperASHS, which produces isotropic-resolution segmentations of the same structures and is available in the cloud through ITK-SNAP as well as locally.

Troubleshooting Local ASHS

If ASHS fails or the results look wrong:

  • Check that your data meet the requirements of the atlas you are using (ASHS-PMC, ASHS-PMC-T1). In particular, the x and y dimensions of the T2-weighted image must be larger than the z dimension.
  • Look at the ASHS output (nohup.out) for the first error message.
  • Check the QC images in the qa subdirectory of the working directory to see whether registration between the template, T1-MRI and T2-MRI succeeded. If the T1 and T2 scans are poorly aligned, register them manually in ITK-SNAP and save the transform in Convert3D format.
  • When running on a cluster, make sure that jobs are actually being scheduled (qstat), and that each core has enough memory (at least 2GB).
  • Ask on the ashs-users mailing list.

See the equivalent page for HyperASHS.