First of all, I experienced some difficulties getting the .m file to work, actually I can seem to get any exported files at all – the folder headmodel is not created either. Though I’m getting the option to do the simulation after pressing the wand button – vat files in nifti format is produced during simulation but these files are just black. Is there any options or procedures that needs to be done before?
And I also have some general questions regarding lead-dbs.
I have been thinking about the scenario using post-op CT, however not as common at my institution but performed anyway from time to time.
Sometimes when manually defining the electrode artifact during reconstruction the images is just black – perhaps its because some pre-processing step is incomplete, I think this phenomena only occur when i skip registration and normalization – just change the postop_ct to lpostop_ct.
Usually I ask our neurosurgeon to manually delineate target structure so the only step i need to take is to register them. But I believe that the black scene appears then as well.
Second question. So preferably we do postop MRIs – including a 3D_T1 image and T2w, PD or T2-STIR depending on target. The 3D_T1 is always included and covers the whole brain and cause no problem regarding SAR/B1+rms levels. However, Medtronics updated guidelines give a little bit more space to increase the coverage of the T2w image for example, but not near the T1. But back to the question, do you have any experience segmenting the electrode based on T1w image? I tried it and it seems to work, but having trouble checking cause I don’t get the nifti, of course there should be other ways of confirming but I’m prefer this until I found something better.
And have I understood it correctly that the normalization step is only for getting structures from template to my images. So if I get the manually, this should be necessary? Or would it affect the reconstruction of the electrodes?
And thanks for a really nice software, I’m really curious about it.