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help > RE: Batching (Command Line version?)
Aug 17, 2019 11:08 AM | Martin Styner
RE: Batching (Command Line version?)
Great! This is clearly a bug in
Auto-EACSF in that (could be an issue of ABC, rather than
Auto-EACSF).
The issue is that rather than removing all extensions from a filename to generate the output filename (image.nii.gz => image), here only one extension is removed (image.nii.gz => image.nii) and then downstream in the workflow other tools do not find the expected output. This is probably due to that my lab prefers the use of NRRD (.nrrd) and thus there is only one extension.
So, your work-around is great, but we need to fix this. I added this as an issue/bug to the tracker https://github.com/NIRALUser/auto_EACSF/issues/8
Martin
Originally posted by cccoleman:
The issue is that rather than removing all extensions from a filename to generate the output filename (image.nii.gz => image), here only one extension is removed (image.nii.gz => image.nii) and then downstream in the workflow other tools do not find the expected output. This is probably due to that my lab prefers the use of NRRD (.nrrd) and thus there is only one extension.
So, your work-around is great, but we need to fix this. I added this as an issue/bug to the tracker https://github.com/NIRALUser/auto_EACSF/issues/8
Martin
Originally posted by cccoleman:
Originally posted by cccoleman:
I figured out what was going on
here. Our T1 image has an extension of ".nii.gz".
This leads to a skullstripped file ending in " .nii_stripped.nrrd"
It looks like that ".nii" in the stripped filename is confusing ABC, leading it to generate a label file ending in "_labels_EMS.nrrd" instead of "_stripped_labels_EMS.nrrd"
Simply unzipping the file before we begin solves this problem.
Looks like things are running smoothly. For future users visiting this thread, my batch script is attached.
.... failure to read the
"_stripped_labels_EMS.nrrd" file.
We _do_ have an image in the ABC_Segmentation folder called 100604-200_1_OwlOrient_labels_EMS.nrrd which is skullstripped..
We _do_ have an image in the ABC_Segmentation folder called 100604-200_1_OwlOrient_labels_EMS.nrrd which is skullstripped..
This leads to a skullstripped file ending in " .nii_stripped.nrrd"
It looks like that ".nii" in the stripped filename is confusing ABC, leading it to generate a label file ending in "_labels_EMS.nrrd" instead of "_stripped_labels_EMS.nrrd"
Simply unzipping the file before we begin solves this problem.
Looks like things are running smoothly. For future users visiting this thread, my batch script is attached.
Threaded View
Title | Author | Date |
---|---|---|
cccoleman | Aug 12, 2019 | |
cccoleman | Aug 17, 2019 | |
cccoleman | Aug 17, 2019 | |
Martin Styner | Aug 17, 2019 | |
Martin Styner | Aug 12, 2019 | |
cccoleman | Aug 15, 2019 | |
Martin Styner | Aug 16, 2019 | |