Population connective field modeling reveals retinotopic visual cortex organization in utero

• creates registration from fsaverage to individual surfaces¹
• resamples template of visual areas to individual surfaces
• projects functional data to individual surfaces
• applies cortical connective field model to functional data

Prerequisites

Data and templates

• dHCP fourth release data²
• The Lifespan Human Connectome Project Development (HCP-D) 2.0 data ³
• transformations from individual anatomical volume space to group anatomical volume space⁴
• 40 weeks anatomical template in volume space (must be the one that corresponds to the transformation)⁵
• target surface template⁶
• fsaverage subject from freesurfer⁷
• Developing Human Connectome Project spatio-temporal surface atlas of the fetal brain ⁸
• HCP templates "standard mesh atlases"⁹

Software

• newMSM (v0.6.3-BETA) installation¹⁰
• workbench command (v2.0.0) installation¹¹
• MIRTK (v0.20231123) installation¹²
• FSL (v6.0.3) installation, callable from command line¹³

Code avaliabilty

All data analysis was performed with custom software using Python 3.11 and various third-party packages (matplotlib 3.8.3, numpy 1.26.3, pandas 2.2.0, scipy 1.12.0, and nibabel 5.2.0). Brain surfaces were visualized with nilearn (0.10.4).

Data availability

The data for this study are available after institutional registration through public links in the National Institute of Mental Health Data Archive (NDA). Prenatal and neonatal data are available at https://nda.nih.gov/edit_collection.html?id=3955. Adolescent and adult data are available at https://nda.nih.gov/edit_collection.html?id=2846.

Notes

• Please change the path before you run the code

dHCP dataset (prenatal and neonates)

for prenatal dataset, run 01_dataprep/alignment/separte_nii_to_gii.py first before run the program. run run_all.py which contains codes in (01_dataprep, 02_ccfanalysis, 03_retinotopyanalysis)

HCP dataset

run 00_HCP/HCP_file_prep.sh first before run the program. run 00_HCP/HCP_run_all.py

Group comparison

see scripts in 03_retinotopyanalysis

Visualization

see scripts in 04_visualization

Footnotes

1. adapted from dHCP template alignment repo ↩

2. Developing Human Connectome Project ↩

3. Human Connectome Project Development ↩

4. included in the dHCP data ↩

5. The group volumetric atlas used in the dHCP second release is called 'dhcp-volumetric-atlas-groupwise'. Alternatively, the same atlas can be downloaded from Sean Fitzgibbon's 'augmented version'. ↩

6. The dHCP project has published the dhcpSym atlas, which can be used here. ↩

7. included in a freesurfer installation at $FREESURFER_HOME/subjects/fsaverage ↩

8. Developing Human Connectome Project spatio-temporal surface atlas of the fetal brain (https://doi.gin.g-node.org/10.12751/g-node.qj5hs7/) ↩

9. Human Connectome Project templates can be downloaded from the HCPpipelines repo ↩

10. newMSM runs on FSL and can be installed from Renato Besenczi's github repo newMSM. ↩

11. Human Connectome Project Workbench Command ↩

12. Medical Image Registration ToolKit MIRTK, needs root access for installation. ↩

13. fsl installation link (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation) ↩