Hi Jane,

You are correct, the images should be aligned to the ACPC line. However, since you are providing your own mask we need to make sure it is in the right space. 

Let's make sure the correct configuration is being used.
Are you using the rigid registration option? If it is the case, the output of this step creates files with prefix _stx.nrrd, make sure your brainmask is aligned with those. 
Also, if you are providing your own mask, the 'Perform automatic skull-stripping' option on the second tab should be unchecked.
The skull stripping is performed regardless, i.e., using the computed mask or your own mask.

Finally, let's take a look at the file _labels_EMS.nrrd, this is the output of the tissue segmentation step. The tissue segmentation is key to compute the Final_QCistern output. There are 2 steps here, a non-rigid registration to the segmentation atlas followed by ABC algorithm to compute the tissue classes.

Please check the inputs to the ABC algorithm in the ABCParams.xml file and also the intermediate outputs of this step.

The final steps will use the brainmask and the tissue segmentation to compute the QCistern file.

Please let me know how it goes.


Originally posted by Chieh-En Tseng: