====== Surface-based Analysis (cifti) ======

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

===== 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''

</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>