├── .gitattributes ├── LICENSE ├── MDA_Agenda.md ├── MniAgenda.html ├── MniAgenda.md ├── README.R ├── README.md ├── REFERENCES.bib ├── antsMni.Rmd ├── data ├── 101_aal.nii.gz ├── 101_pcasl.nii.gz ├── 101_prob1.nii.gz ├── 101_prob2.nii.gz ├── 101_prob3.nii.gz ├── 101_prob4.nii.gz ├── 101_prob5.nii.gz ├── 101_prob6.nii.gz ├── 101_seg.nii.gz ├── 101_t1.nii.gz ├── JLF │ ├── ilist1.nii.gz │ ├── ilist10.nii.gz │ ├── ilist11.nii.gz │ ├── ilist12.nii.gz │ ├── ilist13.nii.gz │ ├── ilist14.nii.gz │ ├── ilist15.nii.gz │ ├── ilist16.nii.gz │ ├── ilist17.nii.gz │ ├── ilist18.nii.gz │ ├── ilist19.nii.gz │ ├── ilist2.nii.gz │ ├── ilist20.nii.gz │ ├── ilist21.nii.gz │ ├── ilist22.nii.gz │ ├── ilist23.nii.gz │ ├── ilist24.nii.gz │ ├── ilist25.nii.gz │ ├── ilist26.nii.gz │ ├── ilist27.nii.gz │ ├── ilist28.nii.gz │ ├── ilist29.nii.gz │ ├── ilist3.nii.gz │ ├── ilist30.nii.gz │ ├── ilist31.nii.gz │ ├── ilist32.nii.gz │ ├── ilist33.nii.gz │ ├── ilist34.nii.gz │ ├── ilist35.nii.gz │ ├── ilist36.nii.gz │ ├── 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slist26.nii.gz │ ├── slist27.nii.gz │ ├── slist28.nii.gz │ ├── slist29.nii.gz │ ├── slist3.nii.gz │ ├── slist30.nii.gz │ ├── slist31.nii.gz │ ├── slist32.nii.gz │ ├── slist33.nii.gz │ ├── slist34.nii.gz │ ├── slist35.nii.gz │ ├── slist36.nii.gz │ ├── slist37.nii.gz │ ├── slist38.nii.gz │ ├── slist39.nii.gz │ ├── slist4.nii.gz │ ├── slist40.nii.gz │ ├── slist41.nii.gz │ ├── slist42.nii.gz │ ├── slist43.nii.gz │ ├── slist44.nii.gz │ ├── slist45.nii.gz │ ├── slist46.nii.gz │ ├── slist47.nii.gz │ ├── slist48.nii.gz │ ├── slist49.nii.gz │ ├── slist5.nii.gz │ ├── slist50.nii.gz │ ├── slist51.nii.gz │ ├── slist52.nii.gz │ ├── slist53.nii.gz │ ├── slist54.nii.gz │ ├── slist55.nii.gz │ ├── slist56.nii.gz │ ├── slist57.nii.gz │ ├── slist58.nii.gz │ ├── slist59.nii.gz │ ├── slist6.nii.gz │ ├── slist60.nii.gz │ ├── slist7.nii.gz │ ├── slist8.nii.gz │ └── slist9.nii.gz ├── JLF_out │ ├── jlfout_pred.nii.gz │ ├── jlfout_prob1.nii.gz │ ├── jlfout_prob2.nii.gz │ ├── jlfout_prob3.nii.gz │ ├── jlfout_prob4.nii.gz │ └── jlfout_seg.nii.gz ├── Subjects │ └── PEDS012 │ │ └── 20100813 │ │ ├── PEDS012_20100813_30dir_anatomical.nii.gz │ │ ├── PEDS012_20100813_30dir_fa_anatomical.nii.gz │ │ ├── PEDS012_20100813_AAL.nii.gz │ │ ├── PEDS012_20100813_BrainSegmentation.nii.gz │ │ ├── PEDS012_20100813_CorticalThickness.nii.gz │ │ ├── PEDS012_20100813_MeanCBFWarpedToT1.nii.gz │ │ └── PEDS012_20100813_mprage_t1.nii.gz └── template │ ├── Labels │ ├── PTBP_T1_AAL.nii.gz │ ├── PTBP_T1_Brodmann.nii.gz │ ├── PTBP_T1_JHU.nii.gz │ └── make_priors.sh~ │ ├── PTBP_CBF.nii.gz │ ├── PTBP_Deface.nii.gz │ ├── PTBP_FA.nii.gz │ ├── PTBP_MD.nii.gz │ ├── PTBP_MeanBold.nii.gz │ ├── PTBP_RD.nii.gz │ ├── PTBP_T1_BrainCerebellum.nii.gz │ ├── PTBP_T1_BrainCerebellumExtractionMask.nii.gz │ ├── PTBP_T1_BrainCerebellumMask.nii.gz │ ├── PTBP_T1_BrainCerebellumProbabilityMask.nii.gz │ ├── PTBP_T1_CerebrumProbabilityMask.nii.gz │ ├── PTBP_T1_Head.nii.gz │ ├── Priors │ ├── make_priors.sh │ ├── priors1.nii.gz │ ├── priors2.nii.gz │ ├── priors3.nii.gz │ ├── priors4.nii.gz │ ├── priors5.nii.gz │ └── priors6.nii.gz │ └── crop.R ├── handout ├── antsGithubExamples.Rmd ├── antsHandout.Rmd └── antsHandout.pdf ├── phantomData ├── phantomAwmgm.jpg ├── phantomBwmgm.jpg ├── phantomCwmgm.jpg ├── phantomDwmgm.jpg ├── phantomEwmgm.jpg ├── phantomFwmgm.jpg ├── phantomGwmgm.jpg ├── phantomHwmgm.jpg ├── phantomtemplate.jpg └── phantpredictors.csv ├── registration ├── antsRegistrationIntro.Rmd ├── figures │ └── commandLine.png ├── ndgenStudy.Rmd └── registration.Rmd ├── scripts ├── multiviewEvaluationInNeuroimaging.Rmd └── scripts.Rmd ├── segmentation └── segmentation.Rmd ├── src ├── ANTsLogoSwirl.pdf ├── ANTsLogoSwirl2.pdf ├── ANTsR_Intro.Rmd ├── CorticalAreaAndThickness.Rmd ├── PTBP_Eanat.Rmd ├── PTBP_Intro.Rmd ├── PTBP_MRVRNF.Rmd ├── PTBP_VBM.Rmd ├── PTBP_VBM2.Rmd ├── PTBP_rsfmri.Rmd ├── antsLogo3.png ├── antsLogoBase.png ├── beamerASL.Rmd ├── mystyle.tex ├── phantomMorphometryStudy.R ├── 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