Date: 2022-11-01 RAVE version: 1.0.3.1

Preparation

What's in the preparation steps:

The dcm2niix script consolidate the MRI and CT raw data (series of many DICOM images) into two Nifti-1 (.nii) files.
To bring the MRI and CT datasets into alignment, RAVE calls image registration routines from either AFNI or FSL (the user can specify which).
The MR dataset is skull-stripped and normalized.

By the end of the preparation step, RAVE will create the following data structure:

~/rave_data/raw_dir
└─PAV006
  └─rave-imaging
    ├─coregistration
    ├─fs
    ├─inputs
    ├─log
    └─scripts

Setup

Install RAVE
Create a subject folder in raw_dir. The subject folder must start with letters (a-z, A-Z) and can only include letters and digits (0-9). (For example, YAB, PAV001)
Within the subject folder, create two folders pre-MRI and post-CT
Copy-paste pre-implant MRI files (DICOM or nii) into pre-MRI folder
Copt-paste post-implant CT files (DICOM or nii) into post-CT folder

Create a RAVE subject

Open R program, type the following R command

rave::start_rave2()

You should be able to see RAVE interface

Open Import LFP > Native Structure
Choose/Create a meaningful project name
Select subject that you want to localize (in this example, we use PAV006)
Press Create Subject

You should be able to see a new subject locDemo/PAV006 created inside of data_dir

Surface reconstruction, and CT coregistration

Use the "Search" feature to find Reconstruction & Coregistration module. Open the module

Please make sure the followings are properly configured:

Select the project & subject you have just created
Choose proper pre-implant MRI in the Raw MRI dropdown menu
- If the imaging files are .dcm, you can choose the entire pre-MRI folder
- If the imaging data has .nii format, please choose the .nii file
Choose post-CT in the Raw CT dropdown menu (same as above)
The application paths are correct
- dcm2niix converts DICOM to Nifti. If you have already generated .nii files, you can leave it blank (Optional)
- FreeSurfer home is the home directory of your FreeSurfer software $FREESURFER_HOME (Mandatory)
- FSL home is the home directory of the FSL software $FSL_DIR. (Mandatory if you want to use FSL-flirt to align CT to MRI)
- AFNI home is the AFNI binary path (Mandatory if you want to use AFNI-3dallineate to align CT to MRI)

Press Check data and command-line tools to load data

Convert/Copy MRI & CT files

Click Convert .dcm images to .nii to expand the first panel,
Press Import from RAVE (T1 MRI) and Import from RAVE (CT) buttons respectively

Please wait until the notification is displayed. Make sure you CAREFULLY read the log information when importing .dcm imaging files (sometimes multiple Nifti files will be generated)

Import MRI

This step imports MRI .nii file into RAVE.

Click Surface reconstruction on the left panel to expand the second right panel
Click on Refresh to reload MRI list. Select proper MRI from the dropdown menu

If MRI .nii files are derived from DICOM images, there could be multiple files, the built-in nii viewer will allow you to check the slice counts and voxel sizes.

Select -autorecon1 as the Recon flag, and click Run from RAVE.
- This step will run FreeSurfer recon-all -autorecon1, which only skull-strip and normalize the MRI slices. The step will take about 10 min

Coregistration CT to MRI

Click on CT co-registration to expand the last right panel.

Select a proper CT imaging file
Select FSL if you have fsl-flirt insalled, otherwise AFNI to use 3dallineate

Press Run from RAVE. Wait until coregistration finished. The process will be ~30min - 1hr

dipterix / threeBrain

Surface Reconstruction & Coregistration with RAVE #22