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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
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cspm_project_coreg2mni (48)
In the next window, select a subject, then a scan (either the T1 or the resting state scan in this case).
Click the orange button ‘SPM – Open MNI (reference)’ to open the standard brain in SPM
Then open the subject’s scan (here resting state scan)
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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 “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”)
Check the box “overwrite existing”
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.
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Image out of date - “Save to Selectted Study” now Save to Database”
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You can also open and view the nifti files in MRICRON using the white buttons, which loads faster than SPM.
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Nifti – MNI
Nifti – Raw
Nifti - Project
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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.
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