Donders-Institute / PRESTUS

PREprocessing & Simulations for Transcranial Ultrasound Stimulation package
GNU General Public License v3.0
12 stars 10 forks source link

Dedicated segmentation path option, minor bug fixes, updated simnibs call #2

Closed jkosciessa closed 1 year ago

jkosciessa commented 1 year ago

These updates add the option to specify parameters.seg_path as the location where simnibs' m2m folders will be deposited. I added this path directly to the main script, so did not yet test it out wiht yaml specification. If no seg_path is provided, data_path is used as a default, ensuring backward compatibility.

There are a few other changes:

achetverikov commented 1 year ago

Your last commit seem to be a add hotfix for mni2subjects function, which is already in the code, but for some reason there are conflicts related to previous commits. Could be because I tried to rewrite the emails for @eleonoracarpino in the history. I can merge them, but it would be better I think if you add the commits you mention in your description ('seg_path') so we can see how it matches with other changes I've made and merge everything.

As an additional note, I've made forceqform optional in my code, wouldn't want to force it on the user.

jkosciessa commented 1 year ago

@achetverikov Dumb me, I didn't yet push the changes. The relevant commits are f5873ffa7a76fef05b1f879aa0889346e824ca9e for most of the changes described above, and f4a6c433d7fdd5a39eb922bd48da5a8b3ac5709d for a small bug fix. Let me know if I need to open a new pull request after pushing these commits.

Optional forceqform is of course a better option.

achetverikov commented 1 year ago

Merged! I also moved the checks for parameter.seg_path to load_parameters(). And restored use_donders_hpc flag check in run_segmentation. Was there a particular reason you removed it?