Missing file in the container

[shin1kano]

We are testing MIRACL-ACE workflow using the singularity container. So far unsuccessful.

We have found the following one file is missing in the container.
output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/init_tform.mat

`Error Output:
Initializing registration ...
antsAffineInitializer 3 output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/clar.nii.gz /code/atlases/ara/template/average_template_25um_OBmasked.nii.gz output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/init_tform.mat 1 1 0 500
kill: usage: kill [-s sigspec | -n signum | -sigspec] pid | jobspec ... or kill -l [sigspec]

initializing Allen template
antsApplyTransforms -i /code/atlases/ara/template/average_template_25um_OBmasked.nii.gz -r output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/clar.nii.gz -t output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/init_tform.mat -o output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/init_allen.nii.gz
file /code/atlases/ara/template/average_template_25um_OBmasked.nii.gz does not exist.
Transform file does not exist: output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/init_tform.mat
Exception caught of type 16ConvertException
Exception detail: Unable to read image output_dir/final_ctn_down_20_rca_voxel_size_25/clar_allen_reg/init_allen.nii.gz; IO factory cannot create IO object.`

[jono3030]

Hi @shin1kano, thanks for opening this issue! We were still actively working on the issue that you and I corresponded over through e-mail as well and are currently working on a new version of MIRACL that will hopefully fix the issues that you are experiencing. I'll look into this error as well and keep you updated here.

[iam4tune]

@jono3030 I can share the log (error, and output) as .txt files, if that would help with fixing the issue.

[jono3030]

@iam4tune that would be very helpful - thanks!

[iam4tune]

See errorlog and outputlog files

errorlog.txt
outputlog.txt

[iam4tune]

Hello, I was wondering if there’s an update on this?