Originally posted by Alex Brown:
Hello,

I think I have a similar issue. The MID0 files have viewable outputs but not the EMS_withoutVent_Partial_CSF file or FINAL_QCistern file. The volume summary value is "28". I registered the images to be aligned to the ACPC line and the origin is at the AC (is this what ACPC space means?), I am using my own brainmask, the adult tissue segmentation atlas, and to remove the ventricles I'm using the one year old ventricle mask and T1 template. Is there anything that I should be doing differently to get a viewable output in FINAL_QCistern? I have also tried with my own ventricle mask and looked at the uploaded example as a reference but I still haven't been able to get the correct final output, I would really appreciate any guidance.

I am attaching the FinalMasking folder and FINAL_QCistern files if you could have a look. Thank you for your help!

Best wishes,
Jane