One use case where we could think of how to apply it is after the
Freesurfer segmentation. People want to inspect the white matter mask
that was segmented, and in case, change it and feed the new mask and
re-execute parts of the Freesurfer processing stream. This requires to
convert the mask from .mgz to .nii. We could output the white matter in
any case to some folder and use it for further processing in the
subsequent stage (we output the mask to wm_correction only if the option
is set in the configuration tab).
Maybe it would make sense to split the freesurfer step into two
steps/stages. The commands now are:
1) recon-all -s %s -all -no-isrunning
2) recon-all -s %s -autorecon2-wm -autorecon3 -no-isrunning
It would require to know what 2) minus 1) is in terms of command line
call.
This should certainly be do-able, you'd just need to figure out which
inputs/outputs each of those freesurfer stages requires/creates.
unidesigner
commented
13 years ago
This should certainly be do-able, you'd just need to figure out which inputs/outputs each of those freesurfer stages requires/creates.