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tools:cifti_surfaces [2024/03/15 12:05] – vsydnortools:cifti_surfaces [2025/06/03 16:45] (current) – [Connectome Workbench Tools] vid79
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-====== surface-based analyses ======+====== Surface-based Analysis (cifti) ======
  
-**Working with surface data in R**+Surface files track vertices instead of volumetric voxels. Files are created by tools like [[:tools:xcpd]]. 
 + 
 +===== Types ===== 
 + 
 +citfi files have double extentions like ''*.dscalar.nii''. See [[https://balsa.wustl.edu/about/fileTypes]] for more. From there, highlights are: 
 + 
 +^ dscalar | one or more dense maps of scalar values (e.g., myelin maps, curvature maps) | 
 +^ dtseries | one or more dense timeseries datasets (e.g., fMRI timeseries) or other data at equal intervals | 
 +^ dlabel | one or more dense maps of integer values, plus a ‘label table’ that defines each integer (e.g., one or more parcellations of cerebral cortex, subcortical nuclei, or all grayordinates) | 
 +^ pscalar | one or more parcellated scalar maps (e.g., a parcellated thickness map having uniform thickness within each parcel | 
 +^ ptseries | parcellated timeseries | 
 +^ plabel | one or more parcel maps, where each parcel is identified and colored using a label | 
 + 
 +===== Working with surface data in R =====
  
 See Val's tutorial on github [[https://github.com/PennLINC/surfaces_R_tutorial/blob/main/surface_tools_R.Rmd]] which covers information about cifti files and the fslr surface, types of ciftis/giftis, and how to read, manipulate, write, and visualize dense and parcellated cortical surface data in R See Val's tutorial on github [[https://github.com/PennLINC/surfaces_R_tutorial/blob/main/surface_tools_R.Rmd]] which covers information about cifti files and the fslr surface, types of ciftis/giftis, and how to read, manipulate, write, and visualize dense and parcellated cortical surface data in R
  
-**Working with surface data using Connectome Workbench**+===== Working with surface data using Connectome Workbench ===== 
 + 
 +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 
 + 
 +# 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 
 +sudo apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9 
 + 
 +# 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> 
 + 
 + 
 + 
 +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]]. 
 + 
 +To visualize surface data in workbench, you must load a .surf.gii surface geometry first, and then your surface data. On [[:admin:it:rhea]], [[:tools:templateflow]] has already downloaded some of these to ''/opt/ni_tools/templateflow/tpl-fsLR''. 
 + 
 +<WRAP tip> 
 + 
 +To see your files on a surface: **File > Load** ''/Volumes/Hera/Projects/Habit/mr/tpl/tpl-fsLR_den-32k_hemi-L_midthickness.surf.gii''
  
-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+</WRAP>
  
-Connectome wb_view is a GUI for visualization surface data, which can be downloaded here https://www.humanconnectome.org/software/get-connectome-workbench. To visualize surface data in workbench, you must load a .surf.gii surface geometry first, and then your surface data+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>