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Pickatlas Data Interoperability Joseph Maldjian, MD.

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Presentation on theme: "Pickatlas Data Interoperability Joseph Maldjian, MD."— Presentation transcript:

1 Pickatlas Data Interoperability Joseph Maldjian, MD


3 Pickatlas Software for atlas-based automated hypothesis testing of fMRI data Integrates seamlessly into SPM (99/2/5/8) Provides user with robust selection and combinations of atlas regions


5 Pickatlas R03 EB008670 Published in Neuroimage in July 2003 Cited 383 times Downloaded over 3400 times


7 Atlases Talairach Daemon database –Brodmann area (47 + 28 SC areas) –Lobar –Label –Tissue Type (55 regions) AAL label atlas (116 regions) ICBM label atlas (56 regions) Can easily incorporate additional atlases

8 Next generation Pickatlas Extend interoperability to other packages (FSL, AFNI) Provide 1-stop for atlas-based data inference using SPM engine Incorporate non-human primate atlases


10 Pickatlas Interoperability 1. Image Formats between software packages (SPM, FSL, AFNI) 2. Atlas reference space (MNI, Tal, or something else) 3. SPM import requirements for statistical inference

11 1. Image Formats NIFTI – critical for data interoperability Based on Analyze File Format (348 byte header) Qform/sform fields Defines transformation to “standard” space FSL, SPM use Nifti. AFNI brks?

12 Image Formats Setback: FSL 3.2 and SPM don’t play nice with Nifti in terms of interpretation of qform and sform fields A huge problem for applications that mix software routines (e.g., DTI processing). FSL 4.0 and SPM5/8 Nifti formats are now interchangeable AFNI Brk files: Nifti converter (testing compatibility)

13 2. Atlas reference space Pickatlas uses MNI atlases, but can use any reference space. SPM and FSL use MNI templates: template spaces are interchangeable AFNI uses Talairach space

14 FSL Atlas reference space is identical: MNI Transformations stored in FEAT directory What about non-normalized tmaps? –Apply inverse transform at runtime to pickatlas ROI map

15 AFNI Uses Talairach reference space Option 1: Reslice atlas mask to Talairach space using Lancaster transform at runtime Option 2: Incorporate Talaraich atlases into Pickatlas (inherently available to users)

16 3. SPM import SPM inference engine operates on T- maps and requires smoothness, DOF and.mat file structure FSL smoothness/DOF provided in FEAT directory AFNI information ? User input if not available

17 FSL



20 Thank You!

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