Use mri_label2vol with --fill-ribbon. Note that you can use this to convert the aparc.a2009s into the volume space, then use something like mri_binarize to extract the labels you want.
On 4/16/19 7:52 PM, Sam W. wrote:
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Hi, I created a series of labels with mri_annotation2label (aparc.a2009s labels) and then created a reg file with: tkregister2 --mov mri/rawavg.mgz --noedit --s bert --regheader --reg register.dat and the volume: mri_label2vol --label labels/lh.G_cingul-Post-dorsal.label --temp mri/rawavg.mgz --subject bert --hemi lh --o roi-in-rawavg.nii.gz --proj frac 0 1 .1 --fillthresh .3 --reg register.dat When I load the roi-in-rawavg.nii.gz and the aparc.a2009+aseg.mgz volume in freeview there are parts of the Cingulum in the aparc.a2009+aseg that are not included in the roi-in-rawavg. Probably this is related to the -fillthresh and -proj thresholds. Is there a way to get exactly the same ROI with mri_label2vol as shown in the aparc.a2008+aseg volume? Best regards, Sam
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