Preproccessing Imaging data downloaded using javaws HCP pipelines downloaded to k1201869/hcp/code Need to download MSM binaries https://github.com/ecr05/MSM_HOCR/releases preprocessing instructions at: https://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions Need to copy subjects data from imagingcollection1 to fmriresults/unprocessed/3T Need to amend SetUpHCPPipeline.sh: export HCPPIPEDIR="${HOME}/hcp/code/HCPpipelines-4.2.0-rc.1" ## Set up other environment variables export MSMBINDIR="${HOME}/hcp/code/HCPpipelines-4.2.0-rc.1/MSMBinaries" Need to amend GenericfMRIVOlumeProcessigPipelineBatch.sh and GenericfMRISurfaceProcessigPipelineBatch.sh: StudyFolder="${HOME}//home/k1201869/e_i_modelling/data/HCPEPRelease/imagingcollection01" #Location of Subject folders (named by subjectID) # StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by subjectID) Subjlist="1001_01_MR" #Space delimited list of subject IDs EnvironmentScript="${HOME}/hcp/code/HCPpipelines-4.2.0-rc.1/Examples/Scripts/SetUpHCPPipeline.sh" Tasklist="" Tasklist="${Tasklist} rfMRI_REST1_RL" Tasklist="${Tasklist} rfMRI_REST1_LR" Tasklist="${Tasklist} rfMRI_REST2_RL" Tasklist="${Tasklist} rfMRI_REST2_LR" Run volume then run surface