03. Quanta data

Quanta data

We have downloaded Quanta data set at /space_lin1/quanta.

Subject folder and ID

Each subject has a folder with its ID coded by a 4-digit number. For example, sub-0001 is the ID for the first subject. Its data is at

/space_lin1/quanta/sub-0001

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)

NOTE: These data are transformed to MNI152 space

Structural MRI data

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

For example, /space_lin1/quanta/subjects/sub-0001 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/quanta/scripts. Some of them are:

• Transform volumetric fMRI data from MNI152 space to MNI305 (fmri_vol_2_mni305.m)
• Transform volumetric fMRI data from MNI305 space to FreeSurfer surface (fmri_vol_mni305_2_surf.m)
• Get time series at individual's ventricle and white matter (get_ventricle_wm_regressor.m). This is for removing temporal confounds by regression.
• Functional connectivity based on anatomical parcellation (fconn_resting_roi.m).