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DCAN-Labs / BIBSnet

This BIDS App provides the utility of creating a nnU-Net anatomical MRI segmentation and mask with a infant brain trained model. It can easily be included in other processing pipelines and for circumventing JLF within Nibabies.
https://bibsnet.readthedocs.io/en/latest/
Apache License 2.0
4 stars 8 forks source link

permission error while using the latest image. #138

Closed scott-huberty closed 1 month ago

scott-huberty commented 1 month ago 
          I received a permission error while using the latest image too. Any solution to resolve this?

Originally posted by @shreyagudapati9 in https://github.com/DCAN-Labs/BIBSnet/issues/132#issuecomment-2352504438

@shreyagudapati9 Can you copy and paste the stack trace for the permission error?

shreyagudapati9 commented 1 month ago

@scott-huberty

Screenshot 2024-09-19 at 4 42 09 PM
scott-huberty commented 1 month ago

@shreyagudapati9 Have a look at my instructions in https://github.com/DCAN-Labs/BIBSnet/issues/132#issue-2497628248

and see if you can enter the image and check the permissions of that file models.csv. Feel free to share them here.

shreyagudapati9 commented 1 month ago

@scott-huberty Thank you! Checked the permissions and this is what it shows : -rwxrwx--- 1 root root 713 Aug 14 12:28 /home/bibsnet/data/models.csv

scott-huberty commented 1 month ago

@shreyagudapati9 Looks like you don't actually have the latest image, probably because you have an image with the tag latest in your cache and so docker/singularity doesn't actually pull the updated latest image from docker hub. Try this:

docker pull dcanumn/bibsnet:release-3.4.2

(replace docker with singularity as needed)

Then make sure you point to this image when you run BIBsnet. The permissions on this image should be more permissive (I just confirmed this locally):

docker run -it --entrypoint /bin/bash dcanumn/bibsnet:release-3.4.2

 ls -l /home/bibsnet/data/

drwxrwsr-x 1 77661 12710 4096 Aug 26  2022 MNI_templates
-rwxrwxr-x 1 77661 12710 1370 Aug 26  2022 age_to_avg_head_radius_BCP.csv
-rwxrwxr-x 1 77661 12710  295 Aug 26  2022 dataset_description.json
-rwxrwxr-x 1 77661 12710   32 Aug 26  2022 identity_matrix.mat
drwxrwsr-x 1 77661 12710 4096 Aug 26  2022 look_up_tables
-rwxrwxr-x 1 77661 12710  713 Aug 14 16:28 models.csv
-rwxrwxr-x 1 77661 12710  295 Mar 28 21:29 sidecar_template.json
LuciMoore commented 1 month ago

thanks @scott-huberty !

LuciMoore commented 1 month ago

@shreyagudapati9 did you run into any more errors using the latest version?

scott-huberty commented 1 month ago

@shreyagudapati9 did this solve your issue? Let us know if you are still having problems, otherwise I'll close this ticket at the end of the week.

scott-huberty commented 1 month ago

Closing. @shreyagudapati9 feel free to open another issue if you need to.