#254 (comment)
Item 1 from the linked comment:
Most examples can run with just AA and SPM, except that the presence of FSL is implicit in some places.
In aamod_segment8/diag, a T1 file is read from aap.directory_conventions.fsldir. This gives an error when fsl is not present. The same file is hardcoded in 5 other places in the AA code! In one of those places (aamod_freesurfer_register), also an SPM provided alternative is given. Applying that alternative in aamod_segment8 allows the examples that use segment8 to run to completion.
Proposed: put the hardcoded filename in one place, a getter function that also has something like a allow_alternative input option. And use that function in all 5 places, with the allow_alternative option set depending on where the function is called from.
In aa_provenance, the fls version file is read, without checking if it exists. This gives an error when fsl is not present. Adding a check on the presence of the fsldir and the version file prevents the error.
Proposed: add this check.
#254 (comment)
Item 1 from the linked comment:
Most examples can run with just AA and SPM, except that the presence of FSL is implicit in some places.
In aamod_segment8/diag, a T1 file is read from aap.directory_conventions.fsldir. This gives an error when fsl is not present. The same file is hardcoded in 5 other places in the AA code! In one of those places (aamod_freesurfer_register), also an SPM provided alternative is given. Applying that alternative in aamod_segment8 allows the examples that use segment8 to run to completion.
Proposed: put the hardcoded filename in one place, a getter function that also has something like a allow_alternative input option. And use that function in all 5 places, with the allow_alternative option set depending on where the function is called from.
In aa_provenance, the fls version file is read, without checking if it exists. This gives an error when fsl is not present. Adding a check on the presence of the fsldir and the version file prevents the error.
Proposed: add this check.