Lifespan Human Connectome Project Development (HCP-D) Study

The HCP-D Study planned to enroll 1,300+ healthy children, adolescents, and young adults (ages 5-21). The purpose is to discover how different parts of a child’s brain are connected and how these connections (the “connectome”) change as the brain develops.

License

The NDA  agreement prohibits me from sharing raw MRI data (e.g. T1W, DWI, and SRC.GZ files). After discussion with the NDA program lead, I am allowed to share the “derived” data, including the anisotropy, diffusivities, local fiber orientations, and tractography. This includes the FIB file and the tractography. For other data, you may request access at NDA.

The FIB files and tractography files are shared using Creative Commons Attribution-ShareAlike 4.0 International License.  For those using FIB and tractography files, I would appreciate your mentioning of the contribution of XSEDE resources: TG-CIS200026.

Download

Processing Scripts

1. generate SRC files from NIFTI files

First, copy all NIFTI, bval, bvec files in the same folder and run this script to generate SRC files (one for AP, one for PA)

#!/bin/bash
for sub in $(ls HCD8*98_AP.nii.gz)
do    
    dsi_studio --action=src --source=${sub},${sub:0:25}99_AP.nii.gz
    dsi_studio --action=src --source=${sub:0:25}98_PA.nii.gz,${sub:0:25}99_PA.nii.gz
done

2. TOPUP/EDDY and save corrected SRC files

Correct artifacts using AP and PA SRC files and generate corrected AP-PA combined SRC files. The script needs a number input that allows for running the task using clusters job arrary

#!/bin/bash
subs_ap=$(ls -Lr *AP.nii.gz.src.gz)
subs_ap=(${subs_ap// /})
subs_pa="${subs_ap[$1]:0:28}PA.nii.gz.src.gz"
if [ ! -e $sub_pa ]; then
     echo "." > ${sub_pa}_not_found.txt
else    
     echo "processing ${subs_ap[$1]}"
     dsi_studio --action=rec --source=${subs_ap[$1]} --rev_pe=${subs_pa} --cmd="[Step T2][File][Save Src File]=${subs_pa:0:10}.src.gz"
fi

The following is the job array to run the above script using sbatch. The script needs an the file name of the script to run the job array.

#!/bin/bash
#SBATCH -t 24:00:00
#SBATCH -p RM-shared
#SBATCH -N 1
#SBATCH --ntasks-per-node 8
#SBATCH --mem=15GB
#SBATCH --array=0-999
set -x
sh $1 $SLURM_ARRAY_TASK_ID

3. reconstruction

The following command generate native space FIB files for automatic fiber tracking

dsi_studio --action=rec --source=*.src.gz

The following command generate template space FIB files for correlational tractography

dsi_studio --action=rec --source=*.src.gz --method=7 --template=0 --record_odf=1 --dti_no_high_b=1

4. automatic fiber tracking

The following script for a job arrary to runs fiber tracking on all native-space FIB file.

#!/bin/bash
subs=$(ls -L *.fib.gz)
subs=(${subs// /})
echo "processing ${subs[$1]}"
dsi_studio --action=atk --export_template_trk=1 --source=${subs[$1]}

5. create connectometry database for correlation tractography

The following command create connectometry database from template-space FIB file

dsi_studio --action=atl --source=. --cmd=db --template=../../HCP1065.1mm.fib.gz