Here is an addition to my previous post:

In case of doubt, you can also use the -altas argument of imgcalc, which sometimes works better than -blobs. 
In that case, try the -sdmreg argument to get your image in the right form.
So the commands would be something like:

(1)
./imgcalc.sh YourImageName.nii.gz -sdmreg YourImageNameRegistered

(2)
./imgcalc.sh YourImageNameRegistered.nii.gz -atlas atlas_output

Best,
Matthias

PS: In my previous post, the command:
./imgcalc.sh 1stAnalysis_sdm/YourImageName.nii.gz -blobs blob_output 
can be simplified to:
./imgcalc.sh YourImageName.nii.gz -blobs blob_output
(I just used a file from a subfolder in my original call)