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37. EEG MRI analysis

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Fa-Hsuan Lin edited this page Aug 1, 2023 · 27 revisions

Structural MRI

Reconstruct brain structure using FreeSurfer and T1-weighted MRI (MPRAGE sequence) data. Details are here.

fMRI

Follow the instruction here for fMRI data pre-processing, including the following

  • convert meas.dat into Matlab mat files
  • register between fMRI and structural MRI
  • prepare fMRI data on brain surfaces

The fMRI analysis using Genearal Linear Model can be found here.

Register between anatomical MRI and fMRI

  1. Using only SMS-InI data

-1.a. Prepare an initial registration matrix

First, you need to have an initial registration matrix file, such as this one. If not, please create one as the following:

s002
5
5
0.250000
    0.0421    0.9796    0.1969    1.8653
    0.0262   -0.1982    0.9798  -31.0046
   -0.9988    0.0362    0.0341   -2.7172
         0         0         0    1.0000
round

Note that the first line indicates the subject (in your $SUBJECTS_DIR) to be used as the anatomical template. In this case, it is subject s002. Save this text file as, for example, bb_register_init.dat.

Then, use this script to show the registration between fMRI and anatomical MRI. Remember to check if the subject indicated at the 2nd line of the code matches the subject in bb_register_init.dat.

-1.b. Manually coregister between fMRI and anatomical MRI (FreeSurfer recon) Run [this script] to show fMRI overlaid on structural MRI

-1.c. Run bb_register to get more accurate registration

  1. Using EPI data with sliced matched with SMS-InI reference scans

-2.a. Prepare EPI data [This script file] prepares slices of EPI data matched with SMS-InI reference data.

-2.b. Prepare an initial registration matrix Please refer to step 1.a above for this step.

-2.c. Manually coregister between fMRI and anatomical MRI (FreeSurfer recon) Please refer to step 1.b above for this step.

-2.d. Run bb_register to get more accurate registration

EEG

EEG pre-processing includes

  • suppress gradient and pulse artifacts.
  • calculate event-related potentials (for event-related design).

To do EEG source anaylysis, follow the procedure here.

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