How to name the input files

[venkatbits]

Hi

I am trying to use anat2vessels code
when running data preprocessing step I am getting the following error
python preprocess_imgs.py --t1_dir /home/bits/Desktop/anat2vessels-main/n794/t1w --t2_dir /home/bits/Desktop/anat2vessels-main/n794/t2w --output_dir /home/bits/Desktop/anat2vessels-main/n794/preprocessed --id_delim "_"
File "preprocess_imgs.py", line 74
file_name = f'{subid}_0000.nii.gz'
^
SyntaxError: invalid syntax

I have the folder home/bits/Desktop/anat2vessels-main/n794/ inside which I have kept my t1w and t2w files as t1w.nii.gz and t2.nii.gz what am I doing wrong here

[asagilmore]

Sorry for the late reply here, its unclear why there would be a syntax Error here, and is not reproducible on my local machine.

With that said, the reason for the --id_delim argument is to separate the subject id from other parts of the file name, and copy only that string to the post processed file name. If your files are named only with the id you want to track, you can set this id_delim argument to ".", to split the files at the file extension and copy all of the file name to the post processed files.

Note that you cannot include any _ in the subject id, meaning after splitting with the given id_delim, there should be no _ on the left side. This causes an issue with how nnUNet parses file names.

For your case here, "." should be the right argument.