Hi Steve,
You can use SPM's brainmask.nii as an explicit mask. The file is located within the apriori/ folder. You will need to convert this image to a binary mask using SPM's Imcalc function. There is another method that you can use to create an explicit mask. Please see my response to a similar post here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1009&L=SPM&D=0&1=SPM&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=500866
Hope that helps,
Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: [log in to unmask]<mailto:[log in to unmask]>
________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Steve Masson [[log in to unmask]]
Sent: Thursday, August 18, 2011 8:12 AM
To: [log in to unmask]
Subject: [SPM] Masking with Batch Interface
Dear SPM users,
First, thanks to Tony and James for their answer concerning an activation in an eye. It was really helpful. I'm now trying to apply a mask in my 1st level model. I've never done that.
I use the Batch Interface.
Based on the SPM manual ("A sensible option here is to use a segmentation of structural images to specify a within-brain mask.", p. 67), I choose an image of the segmentation step, the C1*, and put it as an explicit mask in the model specification (see attachment script.png).
It's certainly not the way to go because almost all the significant activations within the brain are gone after masking (see attachment LeftWithMask.png).
Am I choosing the right image to do the masking (cf. C1* image)? Am I doing something else that is incorrect?
Any help will be greatly appreciated!
Regards,
Steve
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