help
help > RE: Batching (Command Line version?)
Aug 17, 2019 07:08 AM | cccoleman
RE: Batching (Command Line version?)
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 | |