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tools:cifti_surfaces [2025/05/27 11:33] – vid79tools:cifti_surfaces [2025/06/03 16:45] (current) – [Connectome Workbench Tools] vid79
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 ===== Working with surface data using Connectome Workbench ===== ===== Working with surface data using Connectome Workbench =====
  
-Connectome workbench has a ton of tools for working with surface data and cifti files. See all of the available workbench commands here [[https://www.humanconnectome.org/software/workbench-command/-cifti-create-dense-timeseries]]+Download connectome workbench using these commands in your terminal \\ 
 +(for ubuntu [[https://neuro.debian.net/pkgs/connectome-workbench.html]]; otherwise [[https://www.humanconnectome.org/software/get-connectome-workbench]])
  
 +<code>
 +# check your release Codename matches (2025-05-27: ubuntu 24.04 = 'noble')
 +lsb_release -a
  
-*Download connectome workbench* using these commands in your terminal (for ubuntu [https://neuro.debian.net/pkgs/connectome-workbench.html]; otherwise [https://www.humanconnectome.org/software/get-connectome-workbench]) +# add repo to get neurodebian packages 
-''wget -O- http://neuro.debian.net/lists/noble.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list'' +wget -O- http://neuro.debian.net/lists/noble.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list 
-''sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9'' +sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
-''sudo apt-get update'' +
-''sudo apt-get install connectome-workbench'' +
-Now you should be able to open files in connectome-workbench with wb_view [file path/file name]+
  
 +# install connectome workbench
 +sudo apt-get update
 +sudo apt-get install connectome-workbench
 +</code>
  
 +Now you should be able to open files in connectome-workbench with ''wb_view [file path/file name]''
  
 +====Connectome Workbench Tools====
 +See all of the available workbench commands here [[https://www.humanconnectome.org/software/workbench-command/-cifti-create-dense-timeseries]]
  
 +<code>wb_command -volume-to-surface-mapping /Volumes/Hera/Projects/mMR_PETDA/group_analysis_ashley/ANTI-SACCADE/Anti_harOx_1mm_gmmask.nii.gz /Volumes/Hera/Projects/Habit/mr/tpl/tpl-fsLR_den-32k_hemi-L_midthickness.surf.gii /Volumes/Hera/Projects/Habit/mr/tpl/anti_ashley_atlas.surf.func.gii -trilinear</code>
  
 +Run ''cifti-parcellate'' on all participants using script ''/Volumes/Hera/Projects/Habit/mr/cifti_parcellate_allsub.bash''
 +<code>wb_command -cifti-parcellate /Volumes/Hera/Projects/Habit/mr/xcpd/prep-25.0.0_type-cifti_fd-0.3_bp-yes/sub-11734/ses-1/func/sub-11734_ses-1_task-rest_run-1_space-fsLR_den-91k_stat-reho_boldmap.dscalar.nii /Volumes/Hera/Projects/mMR_PETDA/group_analysis_ashley/ANTI-SACCADE/Anti_harOx_1mm_gmmask.dlabel.nii COLUMN /Volumes/Hera/Projects/Habit/mr/xcpd/prep-25.0.0_type-cifti_fd-0.3_bp-yes/sub-11734/ses-1/func/sub-11734_ses-1_task-rest_run-1_space-fsLR_den-91k_seg-antisaccadeatlas_stat-reho_boldmap.pscalar.nii</code>
  
  
-==== wb_view ====+ 
 +https://github.com/LabNeuroCogDevel/corticalmyelin_maturation/blob/e95717f6de71103cc24df2ecb6ed315f8acb99a7/results/R1_corticalmyelin_anatomy/myelin_maps/parcellate_MWFmap.sh#L9 
  
 Connectome ''wb_view'' is a GUI for visualization surface data, which can be downloaded here [[https://www.humanconnectome.org/software/get-connectome-workbench]]. Connectome ''wb_view'' is a GUI for visualization surface data, which can be downloaded here [[https://www.humanconnectome.org/software/get-connectome-workbench]].
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 </WRAP> </WRAP>
  
 +wb_view example: 
 +<code> wb_view /Volumes/Hera/Projects/Habit/mr/tpl/tpl-fsLR_den-32k_hemi-L_midthickness.surf.gii /Volumes/Hera/Projects/Habit/mr/xcpd/prep-25.0.0_type-cifti_fd-0.3_bp-yes/sub-11734/ses-1/func/sub-11734_ses-1_task-rest_run-1_space-fsLR_den-91k_stat-reho_boldmap.dscalar.nii /Volumes/Hera/Projects/mMR_PETDA/group_analysis_ashley/ANTI-SACCADE/Anti_harOx_1mm_gmmask.dlabel.nii /Volumes/Hera/Projects/Habit/mr/xcpd/prep-25.0.0_type-cifti_fd-0.3_bp-yes/sub-11734/ses-1/func/sub-11734_ses-1_task-rest_run-1_space-fsLR_den-91k_seg-antisaccadeatlas_stat-reho_boldmap.pscalar.nii</code>