christophbrgr / brats-orchestra Goto Github PK

Hi,

I'm trying to use brats-segment to segment my dataset. I used the command:

brats-segment -t1 $t1_path -t1c $t1c_path -t2 $t2_path -fla $flair_path -d all -o /Volumes/Dati/tmp/BratS_prove/xxx/scan_directory/file.nii.gz -v

where obviously the file "file.nii.gz" does not exist.
This is the output:

DIRNAME is: /Volumes/Dati/tmp/BratS_prove/xxx/scan_directory
FILENAME is: file.nii.gz
Now running a new set of segmentations on input: /Volumes/Dati/tmp/BratS_prove/xxx/scan_directory
/Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4
/Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/results
Called singleSegment with method: all
CALLED MULTISEGMENT
[Orchestra] Segmenting with econib
[Weborchestra][Success]Loaded fileformat: {'t1': 't1.nii.gz', 't1c': 't1c.nii.gz', 't2': 't2.nii.gz', 'fla': 'flair.nii.gz'}
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/t1.nii.gz
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/t2.nii.gz
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/t1c.nii.gz
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/flair.nii.gz
[Weborchestra][Info] Images saved correctly
[Weborchestra][Info] Starting the Segmentation with container econib now
ERROR DETAIL: runContainer() missing 1 required positional argument: 'outputName'

Which could be the problem?

Thanks a lot,

Domenico