--- title: "Statistical Parametric Mapping (SPM)" linkTitle: "SPM" weight: 1 tags: ["SPM", "functional imaging"] author: Steffen Bollmann aliases: - /tutorials/functional_imaging/spm description: > A tutorial for running a functional MRI analysis in SPM. --- # Statistical Parametric Mapping (SPM) A tutorial for running a functional MRI analysis in SPM. > _This tutorial was created by Steffen Bollmann._ > > Email: s.bollmannn@uq.edu.au > > Github: @stebo85 > > Twitter: @sbollmann_MRI > [Getting Set Up with Neurodesk](https://neurodesk.org/getting-started/) This tutorial is based on the excellent tutorial from Andy's Brain book: https://andysbrainbook.readthedocs.io/en/latest/SPM/SPM_Overview.html Our version here is a shortened and adjusted version for using on the Neurodesk platform. ## Download data First, let's download the data. We will use this open dataset: https://openneuro.org/datasets/ds000102/versions/00001/download Open a terminal and use datalad to install the dataset: ``` cd neurodesktop-storage datalad install https://github.com/OpenNeuroDatasets/ds000102.git ```

We will use subject 08 as an example here, so we use datalad to download sub-08 and since SPM doesn't support compressed files, we need to unpack them: ``` cd ds000102 datalad get sub-08/ gunzip sub-08/anat/sub-08_T1w.nii.gz -f gunzip sub-08/func/sub-08_task-flanker_run-1_bold.nii.gz -f gunzip sub-08/func/sub-08_task-flanker_run-2_bold.nii.gz -f chmod a+rw sub-08/ -R ``` The task used is described here: https://andysbrainbook.readthedocs.io/en/latest/SPM/SPM_Short_Course/SPM_02_Flanker.html ## Starting SPM and visualizing the data Start spm12GUI from the Application Menu:

When the SPM menu loaded, click on fMRI and the full SPM interface should open up:

For convenience let's change our default directory to our example subject. Click on `Utils` and select `CD`:

Then navigate to sub-08 and select the directory in the right browser window:

Now let's visualize the anatomical T1 scan of subject 08 by clicking on Display and navigating and selecting the anatomical scan:

Now let's look at the functional scans. Use CheckReg and open run-01. Then right click and `Browse ...`. Then set frames to 1:146 and right click `Select All`

Now we get a slider viewer and we can investigate all functional scans:

Let's check the alignment between the anatomical and the functional scans - use CheckReg and open the anatomical and the functional scan. They shouldn't align yet, because we haven't done any preprocessing yet:

## Preprocessing the data ### Realignment Select `Realign (Est & Reslice)` from the SPM Menu (the third option):

Then select the functional run (important: Select frames from 1:146 again!) and leave everything else as Defaults. Then hit run:

As an output we should see the realignment parameters:

### Slice timing correction Click on `Slice timing` in the SPM menu to bring up the Slice Timing section in the batch editor:

Select the realigned images (use filter `rsub` and Frames 1:146) and then enter the parameters: - Number of Slices = 40 - TR = 2 - TA = 1.95 - Slice order = [1:2:40 2:2:40] - Reference Slice = 1

### Coregistration Now, we coregister the functional scans and the anatomical scan. Click on `Coregister (Estimate & Reslice)` (the third option) in the SPM menu to bring up the batch editor:

Use the Mean image as the reference and the T1 scan as the source image and hit Play:

Let's use CheckReg again and overlay a Contour (Right Click -> Contour -> Display onto -> all) to check the coregistration between the images:

### Segmentation Click the `Segmentation` button in the SPM menu:

Then change the following settings: - Volumes = our coregistered anatomical scan rsub-08-T1w.nii - Save Bias Corrected = Save Bias Correced - Deformation Fields = Forward and hit Play again. ### Apply normalization Select `Normalize (Write)` from the SPM menu:

For the Deformation Field select the y_rsub-08 file we created in the last step and for the Images to Write select the arsub-08 functional images (Filter ^ar and Frames 1:146):

Hit Play again. ### Checking the normalization Use CheckReg to make sure that the functional scans (starting with w to indicate that they were warped: warsub-08) align with the template (found in /opt/spm12/spm12_mcr/spm12/spm12/canonical/avg305T1.nii):

### Smoothing Click the `Smooth` button in the SPM menu and select the warped functional scans:

Then click Play. You can check the smoothing by using CheckReg again:

## Analyzing the data Click on `Specify 1st-level` - then set the following options: - Directory: Select the sub-08 top level directory - Units for design: Seconds - Interscan interval: 2 - Data & Design: Click twice on New Subject/Session - Select the smoothed, warped data from run 1 and run 2 for the two sessions respectively - Create two Conditions per run and set the following: - For Run 1: - Name: Inc - Onsets (you can copy from here and paste with CTRL-V): 0 10 20 52 88 130 144 174 236 248 260 274 - Durations: 2 (SPM will assume that it's the same for each event) - Name: Con - Onsets: 32 42 64 76 102 116 154 164 184 196 208 222 - Durations: 2 - For Run 2: - Name: Inc - Onsets: 0 10 52 64 88 150 164 174 184 196 232 260 - Durations: 2 - Name: Con - Onsets: 20 30 40 76 102 116 130 140 208 220 246 274 - Durations: 2 When done, click the green Play button. We can Review the design by clicking on `Review` in the SPM menu and selecting the SPM.mat file in the model directory we specified earlier and it should look like this:

### Estimating the model Click on `Estimate` in the SPM menu and select the SPM.mat file, then hit the green Play button. ### Inference Now open the `Results` section and select the SPM.mat file again. Then we can test our hypotheses: Define a new contrast as: - Name: Incongruent-Congruent - Contrast weights vector: 0.5 -0.5 0.5 -0.5

Then we can view the results. Set the following options: - masking: none” - p value adjustment to control: Click on “none”, and set the uncorrected p-value to 0.01. - extent threshold {voxels}: 10