Preemptive question re: ANTS custom template use?

[jlhanson5]

Hello mindboggle friends,

I had a bit of a preemptive/planning question for the group...

I was just getting mindboggle setup in my group, and was thinking of using a study-specific template (derived through Nick Tustison's ANTs cook priors script: https://github.com/stnava/ANTs/blob/master/Scripts/antsCookTemplatePriors.sh).

Would use of "custom" priors cause any issues with mindboggle (if I was combining Freesurfer and ANTS segments)? I didn't think so, but then I know there were some registration to template files that mindboggle was looking for.

Any information or thoughts are greatly appreciated!

Thanks much, Jamie.

[binarybottle]

Hello! To be clear, you wish to use the same OASIS-20 joint fusion atlas labels but not the corresponding OASIS-20 Atropos template (on http://www.mindboggle.info/data.html), but wish to create your own template? Creating your own template is a great idea, as it will better represent your population. It would be even better if you were to construct a new atlas to match your own template, but I don't see why you can't go ahead.

You will need to make two changes:

1. When you run antsCorticalThickness.sh with the command in http://mindboggle.readthedocs.io/en/latest/#run-separate-commands, you will need to replace the Atropos TEMPLATE with your own.

2. In the main nipype script (mindboggle/mindboggle/mindboggle), you will need to create and call a new transform (unless you register your template to the default template above):

atropos_to_MNI152_affine = 'OASIS-30_Atropos_template_to_MNI152_affine.txt'

[binarybottle]

Addendum: By running antsCorticalThickness.sh, you will generate four transforms (I just mention one affine transform in (2) above). See mindboggle/mindboggle/mindboggle for details:

# ------------------------------------------------------------------------           
# For transforming volume labels --                                                  
# Make list of ANTs MNI152-to-subject nonlinear transforms                           
# to use Apply_ants_transforms:                                                      
#                                                                                    
# Note regarding Apply_ants_transforms:                                              
# To warp the subject image to the template, one would call                          
# Apply_ants_transforms...-i ${subject} -r ${template}                               
#                       -t ${prefix}SubjectToTemplate1Warp.nii.gz                    
#                       -t ${prefix}SubjectToTemplate0GenericAffine.mat              
# To warp the template image to the subject, one would call                          
# Apply_ants_transforms...-i ${template} -r ${subject}                               
#                       -t ${prefix}TemplateToSubject1GenericAffine.mat              
#                       -t ${prefix}TemplateToSubject0Warp.nii.gz                    
# ------------------------------------------------------------------------