Manual Coreg to MNI Step-by-Step Instructions

Owned by Paul Macey
Last updated: Mar 07, 2022
4 min read

CSPM manual co-registration

Overview

The goal is to find the 6 parameters that align the scan with the template, and save these in the database, linked with the study. CSPM then applies the reorientation (coregistration) using these database parameters at the project “Copy and Coreg”.

Steps

Open MATLAB

Type: spm fmri

Select CSPM toolbox

In the next window, select ‘Projects’:

In the Project window, select your project (HCP) and click the button ‘Manual coreg to MNI’:

 

An error box pops up; the command the button is supposed to run is copied to the clipboard. Click ok and go back to the main MATLAB window. Paste the command from the clipboard and hit the return button.

 

Alternatively, you can skip steps 2-6 and type this command directly into MATLAB, all subject scans in the project will be loaded. Wait.

cspm_project_coreg2mni (48)

 

  1. In the next window, select a subject, then a scan (either the T1 or the resting state scan in this case).

  2. Click the orange button ‘SPM – Open MNI (reference)’ to open the standard brain in SPM

  3. Then open the subject’s scan (here resting state scan)

  1. Details:

    1. The text ‘MNI (ref) “single_subj_t1.nii” ….’ Is the path to the MNI standard brain.

      1. If you hover over the text, it shows the path.

      2. If you right-click, you get the options to either

        1. Open the MNI file; or

        2. Open the folder where the MNI file is stored on the C-drive

Open the MNI scan in SPM by clicking the top orange button (~30 seconds):

 

This window then opens; the MNI file is named single_subj_t1.nii

  1. Next, open the subject image you want to register to standard space using the second orange button “SPM – Open raw (match to MNI)”, named “XXXX_raw.nii”

    1. If you select the T1 image in the left window under “HCP MRI’s”, the T1 will open when you hit this orange button; if you select the resting state on the left, it will open the resting state scan.

 

Using the coordinate box on the left bottom, we want to adjust the position of the brain relative to the MNI brain, including the position and alignment with respect to the cross hairs.

 

  1. When you think you have matched the subject’s scan as closely as possible to the MNI position/orientation, return to the project window and click the orange button “Copy from SPM”

    • This copies the parameters from the SPM window to the GUI, saving you from typing them in. It does not save them in the database yet.

    • Do not “Reorient”! CSPM applies the reorientation when the files are copied to the project folder (“rawimages”)

  2. Check the box “overwrite existing”

  3. Click “Save to Database” (old: “Save to Selected Study”)

NOTE:

The bottom coordinates are retrieved from copying them from the SPM window.

The greyed out values on the top under “Rigid Body Shift” only appear AFTER the actual co-registration. If this subject’s scan has not previously been co-registered the boxes will be empty. “Last saved” shows when changes were applied last.

Image out of date - “Save to Selectted Study” now Save to Database”

You can also open and view the nifti files in MRICRON using the white buttons, which loads faster than SPM.

White buttons open files in MRICRON (shown here), orange buttons in SPM:

  1. Nifti – MNI

  2. Nifti – Raw

  3. Nifti - Project

The project scan gets copied and co-registered only when the "Copy and Coreg" button is clicked for that project. If that has not been done once, then there will be no project file. If the coreg parameters are changed, they will not be applied until the "Copy and Coreg" is clicked again.