Step 1: Data preprocessing

The first step is very important for the following analysis steps. Please follow our instructions to prepare your data.

System requirements

Windows 10.

CPU with 4 cores and 16GB RAM are enough.

Install Matlab, default setting is suitable during Matlab installation
Install third party package SPM12 in Matlab
- download SPM12 zipfile via this link. If thers's no download window prompted up, go to this website and then choose to download SPM12 in the blank of "SPM version".
- unzip SPM12 zipfile to any directory you want, wherein scripts are placed.
- launch Matlab, add the directory of the unzipped file (along with its sub-folders) to the default search path of Matlab.
Install third party package DPABI in Matlab:
- download DPABI zipfile via this link.
- unzip DPABI zipfile to any directory you want.
- launch Matlab, add the directory of the unzipped file (along with its sub-folders) to the default search path of Matlab.
Install third party package NIFTI package, version 20140122 or higher in Matlab:
- download NIFTI zipfile via this link
- unzip NIFTI zipfile to any directory you want.
- launch Matlab, add the directory of the unzipped file (along with its sub-folders) to the default search path of Matlab.
Download this 1_preprocessing folder, and utils folder, spmutils folder to your device, and add utils folder and spmutils folder to the default search path of Matlab.

Organize the paired T1-MRA volumes the way we did (!!Very important). Suppose you got 1k pairs. It is suggested to name each T1 file as Subject+number-T1.nii, and the paired MRA file as project+number-MRA.nii. Then put these paired files in the imgs folder like this:
```
T1/
├── Subject0001/
│   ├──Subject0001-T1.nii
├── Subject0002/
│   ├──Subject0002-T1.nii
├── ...

MRA/
├── Subject0001/
│   ├──Subject0001-MRA.nii
├── Subject0002/
│   ├──Subject0002-MRA.nii
├── ...
```
A subset consisting of 2 paired T1-MRA volumes was provided in the imgs folder as examples to show the whole procedure. Notably, before running this pipeline, image files with .nii.gz format should be converted to .nii format first.
Run main_T1_preprocessing.m:
To extract masks for grey matter, white matter, and cerebral spinal fluid, which help create deformation fields between individual and MNI space in Step 3.
Run main_arrange_MRAfiles.m:
This script will copy the original MRA file from each subject to a target direcroty ./imgs/rawMRAs, which can be input to the segmentation model.