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Update README.md
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HaiyangJin authored Nov 16, 2021
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Expand Up @@ -58,11 +58,11 @@ As most of the functions in this toolbox call FreeSurfer commands which are linu
1. Start a new terminal;
2. Set all the necessary global environment variables (e.g., `$FREESURFER_HOME`, `$SUBJECTS_DIR` and `$FUNCTIONALS_DIR`) and set up FreeSurfer (the instruction is available on the [FreeSurfer website](https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration));
3. Start Matlab in the *same* terminal by running `path-to-matlab-folder/bin/matlab` in the terminal. [You may also add the `path-to-matlab-folder/bin` to `$PATH` by following [this instruction](https://apple.stackexchange.com/questions/358687/right-way-to-add-paths-to-path-in-mojave) and run `matlab` in the terminal].
<br>

- **Method 2**:
1. Start Matlab and add all subdirectory of this toolbox to the Matlab `path`;
2. Run `fs_setup('path/to/freesurfer/home');` to set `'path/to/freesurfer/home'` as `$FREESURFER_HOME` and add necessary paths to `$PATH`;
3. Run `fs_subjdir('path/to/subjects/dir');` to set `'path/to/subjects/dir'` as `$SUBJECTS_DIR`;
1. Start Matlab and add all subdirectory of this toolbox to the Matlab `path`;
2. Run `fs_setup('path/to/freesurfer/home');` to set `'path/to/freesurfer/home'` as `$FREESURFER_HOME` and add necessary paths to `$PATH`;
3. Run `fs_subjdir('path/to/subjects/dir');` to set `'path/to/subjects/dir'` as `$SUBJECTS_DIR`;

## Create files needed for FreeSurfer
Make sure the following files have been created properly (at least before running the general linear model (GLM) in FreeSurfer).
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