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nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
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TraitError: Cannot set the undefined 'invert_transform_flags' #46

Closed khamael closed 9 years ago

khamael commented 10 years ago

Traceback (most recent call last): File "/usr/local/bin/mindboggle", line 1850, in xfm.inputs.invert_transform_flags = warp_inverse_Booleans traits.trait_errors.TraitError: Cannot set the undefined 'invert_transform_flags' attribute of a 'ApplyTransformsInputSpec' object.

This happens on my very first run with: mindboggle template --ants_segments template/outputSegmentation.nii.gz --thickness --no_surfaces -n 8

binarybottle commented 10 years ago

My first thought is that perhaps you are missing the ants transforms. Did you run antsCorticalThickness.sh with the -t flag (see http://mindboggle.info/users/README.html)?:

antsCorticalThickness.sh -d 3 -a IMAGE -o PREFIX \ -e OASIS-30_Atropos_template/T_template0.nii.gz \ -t OASIS-30_Atropos_template/T_template0_BrainCerebellum.nii.gz \ -m OASIS-30_Atropos_template/T_template0_BrainCerebellumProbabilityMask.nii.gz \ -f OASIS-30_Atropos_template/T_template0_BrainCerebellumExtractionMask.nii.gz \ -p OASIS-30_Atropos_template/Priors2/priors%d.nii.gz

You can use --no_ants_transforms with Mindboggle if you do not have the ANTs transforms (the volume will be labeled using FreeSurfer labels but not ANTs labels).

(Shouldn't your ants output be BrainSegmentation.nii.gz rather than Segmentation.nii.gz?)