Hi!
I’ve tried to run the “5ttgen hsvs” algorithm based on the recon-all output directory from FreeSurfer v. 7.1.0. However, brain stem segmenting / cropping failed; I received the following error message:
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[…]
5ttgen: [100%] Combining and smoothing corpus callosum segmentation
5ttgen: [ 80%] Segmenting and cropping brain stem…
5ttgen: [ERROR] Unhandled Python exception:
5ttgen: [ERROR] ValueError: min() arg is an empty sequence
5ttgen: [ERROR] Traceback:
5ttgen: [ERROR] /usr/local/bin/5ttgen:58 (in execute())
5ttgen: [ERROR] alg.execute()
5ttgen: [ERROR] /usr/local/mrtrix3/lib/mrtrix3/_5ttgen/hsvs.py:437 (in execute())
5ttgen: [ERROR] fourthventricle_zmin = min([ int(line.split()[2]) for line in run.command(‘maskdump 4th-Ventricle.mif’)[0].splitlines() ])
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I hypothesized that there might have been some label changes associated with the fourth ventricle in FS v. 7.1.0 as compared to v. 6, so next, I tried running the same command with the recon-all output from FS v. 6. Indeed, that worked fine. Did anyone encounter similar problems and has found a solution for the issue?
Thanks,
Marlene.