search

neuronets / kwyk

Knowing what you know - Bayesian brain parcellation
https://doi.org/10.3389/fninf.2019.00067
Apache License 2.0
20 stars 9 forks source link

allow using infile path in output. #30

Closed satra closed 2 years ago

satra commented 2 years ago

@Hoda1394 - this should allow using the input name. but the README needs to be improved to indicate how to use this.

i haven't actually tested this.

Hoda1394 commented 2 years ago

I will modify the README.

Hoda1394 commented 2 years ago

@satra - I tried to test it. it seems that it does not solve the multiple infiles issue if all infiles are in the same folder since we only give one prefix for all infiles.

satra commented 2 years ago

@Hoda1394 - ah indeed. we need to support using the name of the infile in the prefix and we were trying to avoid detecting what type of file it is to remove the extension. let me do one more thing.

satra commented 2 years ago

here is a bit of a variant. uses the infile name.

Hoda1394 commented 2 years ago

yes, we need to use the infile name. I think, now it works.

Hoda1394 commented 2 years ago

@satra - it is not clear to me what should the user enter as the value for the base? shouldn't it be a flag?

satra commented 2 years ago

if say the files are at some location /path/to/location/bidsdataset/sub-1/anat/T1.nii.gz the user could provide --base /path/to/location/bidsdataset/. this would remove that from the name. perhaps base is a terrible word for this operation. --stripstr may be a better keyword.