Hi Rachel –
There are a few other flags that need to be set to run cerebro. If you look at the cortical extraction script distributed with BrainSuite, which is probably located at /Applications/BrainSuite15b/bin/cortical_extraction.sh on your machine, there is a line for cerebro:
${BrainSuiteBin}cerebro $VERBOSE $ATLASES -i ${basename}.bfc.$EXT \
-l ${basename}.hemi.label.$EXT -m ${basename}.mask.$EXT -o ${basename}.cerebrum.mask.$EXT \
-c 2 –air ${basename}.air –warp ${basename}.warp ${CEREBROOPTIONS}
Replacing these with the arguments from your command and ignoring some empty variables yields:
cerebro –atlas ${workingdir}/inia19-t1-brain_16bit.img –atlaslabels ${workingdir}/inia-struct.img \
-i e3834_OxM130_AP.nii -o ${workingdir}/e3834_OxM130_AP.cerebrum.mask.nii.gz \
-l ${basename}.hemi.label.$EXT -m ${basename}.mask.$EXT \
-c 2 –air ${basename}.air –warp ${basename}.warp
The -c 2 flag is the one that should fix your issue (it controls the cost function used by AIR during the linear registration step).
You will need the other flags to complete the cortical extraction and SVReg labeling process.-l and -m save the hemisphere labels and cerebrum mask, which are used later for hemisphere splitting and pial surface expansion. The .air and .warp files save the transformation files and are used to initialize parts of the SVReg registration.
You could also edit the cortical extraction script to change the atlas files. These lines (38-40) are where it is specified.
ATLAS=”${BrainSuiteDir}/atlas/brainsuite.icbm452.lpi.v08a.img”
ATLASLABELS=”${BrainSuiteDir}/atlas/brainsuite.icbm452.v15a.label.img”
ATLASES=”–atlas ${ATLAS} –atlaslabels ${ATLASLABELS}”
Let us know if this solves your issue.
thanks,
David