missing 1 required positional argument: 'outputName'

[renero69]

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

[neuronflow]

I believe we fixed this in BTK the continuation of this repo? @christophbrgr ?

https://github.com/neuronflow/BraTS-Toolkit

[renero69]

Thanks a lot,

I installed the last version. Please, let me know if I have to do something

Domenico

Il giorno mar 14 set 2021 alle ore 21:02 neuronflow < @.***> ha scritto:

I believe we fixed this in BTK the continuation of this repo? @christophbrgr https://github.com/christophbrgr ?

https://github.com/neuronflow/BraTS-Toolkit

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/christophbrgr/brats-orchestra/issues/1#issuecomment-919433502, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIWKIYFGZBDQGBVLMZ324XDUB6L3DANCNFSM5EADW6WA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[renero69]

Dear all,

As I told you in the previous email I installed the last version but I can't resolve the issue (missing 1 required positional argument: 'outputName').

Could you please suggest how to resolve it?

Thank you

Domenico

Il giorno mar 14 set 2021 alle ore 21:02 neuronflow < @.***> ha scritto:

I believe we fixed this in BTK the continuation of this repo? @christophbrgr https://github.com/christophbrgr ?

https://github.com/neuronflow/BraTS-Toolkit

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/christophbrgr/brats-orchestra/issues/1#issuecomment-919433502, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIWKIYFGZBDQGBVLMZ324XDUB6L3DANCNFSM5EADW6WA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.