02. HCP data

Human connectome project (HCP)

We have downloaded HCP young adult 1200 data set at /space_lin1/hcp. Details for HCP can be found here.

Subject folder and ID

Each subject has a folder with its ID coded by a 6-digit number. For example, 100206 is the ID for the first subject. Its data is at

/space_lin1/hcp/100206

fMRI "raw" data

We have downloaded the "preprocessed data". These are fMRI data in nii.gz format:

• rfMRI_REST1_LR_hp2000_clean.nii.gz (resting-state fMRI, run1, phase encoding: left-right)
• rfMRI_REST1_RL_hp2000_clean.nii.gz (resting-state fMRI, run1, phase encoding: right-left)
• rfMRI_REST2_LR_hp2000_clean.nii.gz (resting-state fMRI, run2, phase encoding: left-right)
• rfMRI_REST2_RL_hp2000_clean.nii.gz (resting-state fMRI, run2, phase encoding: right-left)
• tfMRI_EMOTION_LR.nii.gz (tasked fMRI; emotion task)
• tfMRI_SOCIAL_LR.nii.gz (tasked fMRI; social task)
• tfMRI_WM_LR.nii.gz (tasked fMRI; working memory task; phase encoding left-right)
• tfMRI_WM_RL.nii.gz (tasked fMRI; working memory task; phase encoding right-left)

Structural MRI data

All subjects have Freesurfer reconstruction at /space_lin1/hcp/subjects.

For example, /space_lin1/hcp/subjects/100206 is the FreeSurfer reconstruction files for subject 100206. It has the following folders:

• label
• mri
• surf
• stat
• scripts
• tmp
• touch

The most commonly used data are surface models in the surf folder. MRI data, including volume segmentation labels (such as .aseg files), in the mri folder. Cortical parcellation/segmentation files (such as .label files) are at label folder.

Please refer to FreeSurfer outputs for further info.

Preprocessing scripts

Scripts for fMRI data preprocessing are at /space_lin1/hcp/scripts. Some of them are:

• Get HCP data as a script: (get_tfmri_wm_file.m; task-fMRI, working memory task)
• Hippocampus segmentation: (hippocampus_seg_script1.m)
• Get time series at ventricles and the white matter as confound regressors in fMRI analysis: (get_native_ventricle_regressor_rest.m; this one is for the resting-state fMRI analysis).
• Register between fMRI and structural MRI: (register_script1.m; This one creates a 12-parameter rigid-body transformation matrix).
• Paint fMRI volume onto brain surfaces (as STC files): (vol2surf_processed_rest_script0.m; This one is for the resting-state fMRI analysis).