---------------- 1. HEADER ---------------- HCP_ICA_MATCHING TOOLBOX, VERSION 1.0 CREATED BY MARLENE TAHEDL, TECHNIAL UNIVERSITY OF MUNICH VERSION 1.0, RELESED AUGUST 2020 PLEASE REPORT ISSUES TO marlene.tahedl@tum.de ---------------- 2. ABOUT ---------------- An automated pipeline for obtaining labeled ICA-templates corresponding to functional brain systems #######ADD DOI####### WITH THIS TOOLBOX, THE BEST MATCHING GROUP-ICA COMPONENT FROM THE HUMAN CONNECTOME'S 1200 SUBJECT RELEASE (TOTAL: 690 COMPONENT MAPS) IS IDENTIFIED FOR A GIVEN INPUT MAP. INPUT CAN BE ANY STATISTICAL BRAIN MAP BOTH IN NIFTI (IN MNI 152 2MM SPACE) OR CIFTI (.dscalar, 32k MESH RESOLUTION) FILES. OUTPUTS CAN BE NIFTI OR CIFTI. ---------------- 3. PREREQUISITES ---------------- - RUNNING VERSION OF MATLAB (TESTED FOR VERSIONS 2018 AND LATER), INCLUDING STATISTICS TOOLBOX (TO USE WITH THE MATLAB FUNCTION "corr"). NOTE THAT ALTERNATIVELY, THE FUNCTION "cosmo_corr" CAN BE USED FROM THE COSMOMVPA TOOLBOX (SEE BELOW). HOWEVER, IN THAT CASE, THE USER NEEDS TO REPLACE ANY "corrs" IN THE FUNCTIONS identifiy_best_match_for_all_dimensionalities.m and correlate_input_to_specifi_dimensionality.m with "cosmo_corr". - FOR USING NIFTI FILES WITH THE TOOLBOX (EITHER INPUT OR OUTPUT): CoSMoMVPA toolbox. PLEASE DOWNLOAD THAT TOOLBOX AT https://github.com/CoSMoMVPA/CoSMoMVPA AND PLACE THE DIRECTORY HCP_ - FOR USING CIFTI FILES WITH THE TOOLBOX * RUNNING VERSION OF CONNECTOME WORKBENCH: DOWNLOAD FROM https://www.humanconnectome.org/software/get-connectome-workbench * MATLAB TOOLBOX FROM HCPpipelines: DOWNLOAD FROM https://github.com/Washington-University/HCPpipelines/blob/master/global/matlab ---------------- 4. USAGE ---------------- 1. DOWNLOAD THE TOOLOBX (I.E. THE ENTIRE DIRECTORY "HCP_ICA_matching") FROM OSF: https://osf.io/mek47/ 2. IF NECESSARY, UNZIP THE DIRECTORY HCP_ICA_matching. PLACE IT WHEREVER YOU WANT TO USE IT ON YOUR SYSTEM. 3. FOR WORKING WITH NIFTI FILES (INPUT OR OUTPUT), DOWNLOAD THE COSMOMVPA TOOLBOX (SEE SECTION 3, "PREREQUISITES", FOR DOWNLOAD LINK). PLACE THE ENTIRE COSMOMVPA DIRECTORY INTO THE MAIN TOOLBOX DIRECTORY ("HCP_ICA_matching"). 4. FOR WORKING WITH CIFTI FILES (INPUT OR OUTPUT), DOWNLOAD THE MATLAB FUNCTIONS FROM THE HCPpipleines (SEE SECTION 3, "PREREQUISITES", FOR DOWNLOAD LINK). PLACE THE ENTIRE "matlab" DIRECTORY INTO THE MAIN TOOLBOX DIRECTORY ("HCP_ICA_matching"). 5. FOR WORKING WITH CIFTI FILES (INPUT OR OUTPUT), DOWNLOAD RUNNING VERSION OF HCP'S WORKBENCH (SEE SECTION 3, "PREREQUISITES", FOR DOWNLOAD LINK). PLACE THIS TOOLBOX ONTO YOUR COMPUTER (E.G. APPLICATIONS) AND CHANGE THAT PATH ACCORDINGLY IN THE MATLAB FUNCITON OF THIS TOOLBOX "identifiy_best_match_for_all_dimensionalities.m" IN LINE 112! 6. NOW YOU'RE READY. JUST INPUT THE PATH TO THE INPUT STATISTICAL BRAIN MAP OF INTEREST (MNI 152 2MM SPACE FOR NIFTI FILES OR 32K MESH RESOLUTION .DSCALAR FILE FOR CIFTI FILES). SPECIFY INPUT AND OUTPUT FILETYPES AND GO! ALSO SEE HELP FUNCTION FROM identifiy_best_match_for_all_dimensionalities.m FOR FURTHER USAGE DETAILS. ---------------- 4. CONCLUDING NOTES ---------------- THE TOOLBOX COMES WITH GROUP-ICA TEMPLATES FROM THE HUMAN CONNECTOME PROJECT [HCP] (https://db.humanconnectome.org/data/projects/HCP_1200). FOR FURTHER NOTES ON THE HCP DATA, SEE THEIR PTN RELEASE DOCUMENTATION AT https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP1200-DenseConnectome+PTN+Appendix-July2017.pdf. THE HCP-MAPS ARE RE-DISTRIBUTED HERE WITH PERMISSION. IF YOU MAKE USE OF THIS TOOLBOX IN YOUR RESEARCH, PLEASE CITE - Tahedl, M., & Schwarzbach, J. V., (2023). An automated pipeline for obtaining labeled ICA-templates corresponding to functional brain systems. Human Brain Mapping (published online). https://doi.org/10.1002/hbm.26435