mindboggle input by default is looking for MRImgh.inputs.template = '%s/mri/orig/001.mgz' which by definition doesn't exist for data processed by the FreeSurfer longitudinal pipeline(v5.3).
Unless there is some reason to use the original, uncorrected T1 it seems better to use MRImgh.inputs.template = '%s/mri/T1.mgz'
/mri/T1.mgz is also the input to the antsCorticalThickness.sh command listed in the mindboggle instructions.
mindboggle input by default is looking for
MRImgh.inputs.template = '%s/mri/orig/001.mgz' which by definition doesn't exist for data processed by the FreeSurfer longitudinal pipeline(v5.3).Unless there is some reason to use the original, uncorrected T1 it seems better to use
MRImgh.inputs.template = '%s/mri/T1.mgz'/mri/T1.mgzis also the input to theantsCorticalThickness.shcommand listed in the mindboggle instructions.