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The raw folder contains all of the different data sources referenced for this project. Donwloads were made in Novemember 2020.

The following sections describe the contents of each folder (note: that some cannot be uploaded due to data use agreements)

derivatives/

The derivatives folder was downloaded from the DCAN ABCD data collection https://collection3165.readthedocs.io/en/stable/derivatives/ Using the https://github.com/DCAN-Labs/nda-abcd-s3-downloader

The file structure looks like this:

  • raw/derivatives/
  • raw/derivatives/abcd-hcp-pipeline/...
  • raw/derivatives/freesurfer-5.3.0-HCP/...

The following files were specified using the download tool:

  • derivatives.anat.space-fsLR32k_curv
  • derivatives.anat.space-fsLR32k_myelinmap
  • derivatives.anat.space-fsLR32k_sulc
  • derivatives.anat.space-fsLR32k_thickness
  • derivatives.anat.stats

Due to data use agreements, this folder and the data within cannot be shared here.

nda_rds_201.csv

This folder represents the DEAP rds version 2.0.1 as converted to a csv. Due to data use agreements, this folder and the data within cannot be shared here. In order to create this file, the rds was simply loaded as a dataframe in R and then saved as a csv.

shaefer_cifti/

The shaefer_cifti folder was downloaded from https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/HCP/fslr32k/cifti

The folder was renamed shaefer_cifti, and only 10 files kept, corresponding to the 100 to 1000 Parcels versions, e.g.,

  • raw/schaefer_cifti/Schaefer2018_100Parcels_7Networks_order.dscalar.nii
  • raw/schaefer_cifti/Schaefer2018_200Parcels_7Networks_order.dscalar.nii
  • ...
  • raw/schaefer_cifti/Schaefer2018_1000Parcels_7Networks_order.dscalar.nii

gordon_balsa/

The following files were downloaded from https://balsa.wustl.edu/WK71

  • raw/gordon_balsa/Gordon333_FreesurferSubcortical.32k_fs_LR.dlabel.nii
  • raw/gordon_balsa/Human.Brodmann09.32k_fs_LR.dlabel.nii
  • raw/gordon_balsa/Human.Composite_VDG11.32k_fs_LR.dlabel.nii

hcp_mmp_balsa

The following files were downloed from https://balsa.wustl.edu/WN56

  • raw/hcp_mmp_balsa/Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii
  • raw/hcp_mmp_balsa/Q1-Q6_RelatedParcellation210.R.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii

arslan_box

The Group folder from https://imperialcollegelondon.app.box.com/s/g5q0kyvpqdha5jgofhmiov9ws1ao0hi0/ was downloaded, and renamed arslan_box.

Example file paths:

  • raw/arslan_box/AAL/AAL_L.mat
  • raw/arslan_box/AAL/AAL_R.mat

diedrichsen_lab

The following folder was downloaded from https://github.com/DiedrichsenLab/fs_LR_32

Example files paths:

  • raw/diedrichsen_lab/Desikan.32k.L.label.gii
  • raw/diedrichsen_lab/Desikan.32k.R.label.gii

mist

The following folder was downloaded from https://figshare.com/articles/MIST_A_multi-resolution_parcellation_of_functional_networks/5633638 The parcellations are then re-sampled from this original volumetric space.

difumo

The following folder was downloaded from https://parietal-inria.github.io/DiFuMo/ They represent the highest resolution available for each of the scales of parcellations. The parcellations are then re-sampled from this original volumetric space. These have have in some cases been added with git lfs due to file size.

-raw/difumo/64.nii.gz -raw/difumo/128.nii.gz -raw/difumo/256.nii.gz -raw/difumo/512.nii.gz -raw/difumo/1024.nii.gz

brainnetome

The 1mm volumetric brainnetome atlas was downloaded from http://www.brainnetome.org/resource/

shen

Two shen volumetric parcellations are downloaded from https://www.nitrc.org/frs/download.php/11629/shen_368.zip and https://github.com/canlab/Neuroimaging_Pattern_Masks/tree/master/Atlases_and_parcellations/2013_Shen_Constable_NIMG_268_parcellation

The two downloaded files are both volumetric (and later re-sampled), one (newer) has 268 parcels and the (older) 268.

yeo

The two yeo 7 networks and 17 networks parcellations were downloaded from: https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fs_LR32k

maps_and_parcs

Five different parcellations, economo, economo7, oasis.chubs and shj were downloaded from https://github.com/ucam-department-of-psychiatry/maps_and_parcs/tree/master/Parcellations/FSAverage These parcellations are downloaded in fsaverage space separate for left and right hemispheres.

multi_atlas

Two parcellations, aicha and spn500, were downloaded from https://github.com/faskowit/multiAtlasTT/tree/master/atlas_data with each parcellation within its own folders, but extracted here. These parcellations were downloaded in fsaverage space separate for left and right hemispheres.

neuro_parc

Eight volumetric parcellations were downloaded from https://github.com/neurodata/neuroparc/tree/master/atlases/label/Human

These have have in some cases been added with git lfs due to file size.

  • raw/neuro_parc/CAPRSC_space-MNI152NLin6_res-1x1x1.nii.gz
  • raw/neuro_parc/CPAC200_space-MNI152NLin6_res-1x1x1.nii.gz
  • raw/neuro_parc/Hammersmith_space-MNI152NLin6_res-1x1x1.nii.gz
  • raw/neuro_parc/Juelich_space-MNI152NLin6_res-1x1x1.nii.gz
  • raw/neuro_parc/MICCAI_space-MNI152NLin6_res-1x1x1.nii.gz
  • raw/neuro_parc/Princetonvisual-top_space-MNI152NLin6_res-1x1x1.nii.gz
  • raw/neuro_parc/Slab907_space-MNI152NLin6_res-1x1x1.nii.gz
  • raw/neuro_parc/Slab1068_space-MNI152NLin6_res-1x1x1.nii.gz

standard_mesh_atlases

Downloaded from http://brainvis.wustl.edu/workbench/standard_mesh_atlases.zip

These files are used to generate new random parcellations and during resampling from fsaverage to LR_fs_32k standard space.

fs_LR_32k_label

Downloaded from https://github.com/ThomasYeoLab/CBIG/tree/master/data/templates/surface/fs_LR_32k/label Includes only the medialwall.annot file. This is a mask with 0's indicating where in the fs_LR_32k space there is medial wall.