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5ttgen fsl: More changes to FIRST error detection #1124

Lestropie opened this Issue Sep 13, 2017 · 1 comment


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Lestropie commented Sep 13, 2017

As discussed in #1070 after the relevant merge.

A local user managed to produce this same fault in a one-off, but it did not reproduce when we tried again... will find out soon enough if repeatedly running the script overnight can reproduce the same fault, but this time with more information for me to extract after the fact.

It appears that in some instances, the file first_all_none_firstseg.nii.gz is not produced, despite .vtk files being successfully produced for all structures of interest. In this particular case, one of the jobs generated a vector bounds checking segfault, such that the corresponding mask image was not generated, but it did successfully create the mesh file before that point. Therefore, in the post-execution script, when these mask images are combined together into a single volume, this one image was missing and therefore the fslmerge command failed.

I think the solution is going to have to be:

  • If not using SGE, check for the presence of all .vtk files, and generate an appropriate error if any one file is missing.

  • If using SGE, a modified file.waitFor() function will need to wait based on a list of expected files, preferably updating the terminal text as new files appear. This way if a single segmentation fails, the user will still be left with an error along the lines of "waiting for files (9 of 10 detected)".

Should also move this functionality to lib/mrtrix3/ as much as possible, so that 5ttgen fsl and labelsgmfix can use the same code.

@Lestropie Lestropie added the scripts label Sep 13, 2017

@Lestropie Lestropie self-assigned this Sep 13, 2017


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Lestropie Sep 15, 2017


Initial attempt in branch fsl_checkfirst_function; requires testing.


Lestropie commented Sep 15, 2017

Initial attempt in branch fsl_checkfirst_function; requires testing.

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