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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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mindboggle looking for /mri/orig/001.mgz when /mri/T1.mgz is more appropriate for longitudinal FreeSurfer data? #195

Open jling-NM opened 4 years ago

jling-NM commented 4 years ago

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.