Dear @BraTS2024Participants , It has come to our attention that the instructions for the MLCube compatibility test were missing the commands for the Meningioma-Radiotherapy and Pathology tasks - apologies for that! The [MLCube Submission Tutorial](https://www.synapse.org/Synapse:syn53708249/wiki/627758) has been updated accordingly, and includes an update to the sample data_prep and evaluation MLCubes (step 2). If you had previously downloaded the sample MLCubes, please redownload the latest one, as that will contain the sample MLCubes for MEN-RT and Path. Good luck!

Created by Verena Chung vchung
@vchung Sure, I just shared the project page "syn59435520" with you as an Admin.
Hello, I started a thread on this topic, but I'm posting here as well in case someone might have a solution. Does anyone know how to handle multiple environments within a single container? We are using multiple models to obtain inferences and perform post-processing on their outputs to generate the final results. Some of these models require different conda environments.
@aasandino , Oh got it, I understand now! Yes, the input, `data_path` is what you would include into SubjectID. That being said, the evaluation MLCube has been configured so that it only looks for the filename to be classified, that is, just the "BraTSPath_*.png" part.
Ok, great! To clarify, the output should be a 2-column CSV file similar to the one uploaded in the validation phase. However, I have another question. If the output path in each row of the CSV file is like this: "~/Validation-Data-anonymized/BraTSPath_Val_12345.png", what would be the path instead of "Validation-Data-anonymized"? It should be the input "data_path,": I mean the path of the folder that contains the images for testing. Thanks!
@aasandino , Apologies, can you please elaborate on what you mean by "if the output file in MLcube will be in the same format, for example ~/datapath/BraTSPath_Image.png. In the MLCube tutorial the output file is a json file"? If it helps at all, the evaluation MLCube will expect your model MLCube to output a 2-column CSV file much like what you had uploaded during the Validation Phase.
@astaraki , Apologies for the trouble you are experiencing. Do you mind sharing your project syn59435520 with me?
Hello, in the validation phase, we upload a 2-column CSV file. I was wondering if the output file in MLcube will be in the same format, for example ~/datapath/BraTSPath_Image.png. In the MLCube tutorial the output file is a json file. So, what would be the rigth format? Thanks!
@vchung Many thanks for your reply. I am afraid but I still cannot push the images: ``` REPOSITORY TAG IMAGE ID CREATED SIZE docker.synapse.org/syn59435520/brats24_gli v1 db2f0ac0f0de 16 minutes ago 17GB docker push docker.synapse.org/syn59435520/brats24_gli:v1 The push refers to repository [docker.synapse.org/syn59435520/brats24_gli] fc85a27d28ac: Preparing ... c5ec52c98b31: Waiting denied: requested access to the resource is denied ```
@astaraki , Thank you for sharing the steps taken to push your Docker image! Everything looks correct to me. The only remaining issue I can think of is that Synapse goes down for maintenance on Sunday evenings (8pm - 12am Pacific Time; Mondays, 5-9am Central European Time). Could you try pushing your Docker image again to see if you are able to now? Let me know
@vchung @ujjwalbaid I am a certified user and I can successfully log in to docker-synapse. Besides that, I am the administrator and the only user of the project "syn59435520" . And of course, I already submitted the paper under my SynID "3450172". Yet, I cannot push the image to the synapse registry. ``` docker login docker.synapse.org --username astaraki ... Login Succeeded ``` ``` docker push docker.synapse.org/syn59435520/brats24_gli:v1 The push refers to repository [docker.synapse.org/syn59435520/brats24_gli] 1ed36152e4d0: Preparing bfadb65f8fe3: Preparing 8239135bec02: Preparing 2c89b3f8b768: Preparing 5f70bf18a086: Preparing d10d9e6fa453: Waiting ... denied: requested access to the resource is denied ``` I appreciate it if you, anyone, could help me find the issue. /Best

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