error when using --modality T2w (with limited FOV)

[springroll-cui]

Hi developers of HippUnfold, I wanted to process data through HippUnfold using a whole-brain T1w and high-resolution T2w of the medial temporal lobe. Below is the relevant code with the T2w modality: singularity run -e /export/software/seahorse/hippunfold/khanlab_hippunfold_latest.sif $arg "${arg}"_hippunfold participant --cores all --modality T2w --t1-reg-template

However, I am given an error message that I don't have much of a clue how to resolve (please see the attached screenshot). I would appreciate any advice/suggestion on what is the error about and what I can do to resolve it! Thank you very much!

[akhanf]

I think maybe the tar file download got interrupted earlier and is now corrupt -- can you try deleting the ...model_best.tar file (from your home directory .cache folder) and re-running?

[springroll-cui]

Hi Dr. Khan, Thank you very much for your suggestion! Sorry it took me a while to respond as I am running HippUnfold on a university server and can't directly modify my home directory where the .cache folder is. I finally found a way around and ran HippUnfold again (with a clean .cache folder), however, I am still having the same problem as shown in the screenshot above. Do you know if there are other things that I can try to resolve this issue? Thank you!

[jordandekraker]

The issue is most likely that your home directory (the default localtion of .cache) is full before the model finishes downloading. You can fix this by adding --env HIPPUNFOLD_CACHE_DIR=/my/new/directoty to your singularity call, specifying a better location to download the model to

[springroll-cui]

Hi Jordan, You are right! I finally moved the data and specified the cache directory to a better location, and now the T2 flag runs successfully! Thank you very much to both you and Dr. Khan for your help!