Closed mshavliuk closed 1 year ago
It might be that the execution of recon-all
needed to be separated from this script, possibly because multiple different segmentations were generated from the same reconstruction, so it didn't make sense to keep it included. Whatever the reason was, it was done before I started meddling with the script, so I can't say for sure.
We could add an additional Boolean argument to the script, such that if it is set, recon-all
is executed as well.
Solved by #193
Suggestions
import_segmentation.zef
has a legacy format and I didn’t manage to use it for import. Let’s replace it with a new one - I would suggest to use theimport_segmentation.zef
but without the first line importingelectrodes.dat
since electrodes are not generated by the script.cp import_segmentation.zef $OUT_DIR/
to thefs2zef.sh
so it produces a ready-to-import directory.fs2zef.sh
files? For me it is very confusing even though I spent many hours converting different MRI scans. If we absolutely need to have so many let's at least use different names for them. I would suggest to keep only on and rename it tofreeSurfer2zeffiro.sh
fs2zef.sh
was performing the reconstruction withrecon-all
based on this code fragment https://github.com/sampsapursiainen/zeffiro_interface/blob/4b5132d6f9eb5bf46dfff710c6a6558870aa3597/scripts/scripts_for_importing/mri2mesh/fs2zef.sh#L38-L48 Why that code was disabled? Do we want to make the convertation process more difficult and require users to runrecon-all
manually? This may lead to unwanted problems and mistakes.