Hi,
I would like to use a binary mask image (skull-stripped, average of all subject's MPRAGE) to restrict the voxels analyzed by SnPM to only those that fall within the boundaries of the mask image. I've used ImCalc in SPM to make the mask in SPM5 (.hdr & .img files) and then loaded it (or so I thought) during the 'set-up' step in SnPM8. However, when I run 'compute' through the GUI, it crashes at snpm_cp.m line 430. I opened the config file produced by 'set-up' and see a 'MASK' variable which points to the correct path location and image file, but using the mask is killing 'compute'. Does anyone know a way to work around this? I have batch code for SPM that forces the use of an analysis mask for 1st level analysis, but it doesn't work when I've tried adapting it for snpm. Admittedly, I'm a terrible programmer so it could just be me... Does anyone know a way to do this? I'm getting a lot of skull artifact that I need to remove from the analysis.
A million thanks in advance,
Jennifer
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