fMRI data preprocessing

Bringing it all together - the batch interface

The SPM batch interface allows you to create workflows for executing multiple processing steps sequentially. This means that you can set up one batch file that contains all preprocessing steps that you want to perform.

1. From the SPM menu panel, select Batch. You will see a pop-up window of an empty batch interface looking like this:

   

2. Now we will start adding each of our preprocessing steps in the order we want them to be executed, starting with realignment.

3. From to top panel of the batch window, select SPM Spatial Realign Realign: estimate & reslice).
4. Now complete the realignment tab of the batch with relevant parameters as in realignment:
   1. Select Data Session.
   2. In the pop-up window, use the left-hand panel to navigate to sub-01/func/.
   3. Use the filter box to load the full time series - type NaN underneath Filter button and press Enter.
   4. In the right-hand panel, select sub-01_task-auditory_bold.nii and press Done.
   5. Back in the batch window, navigate to Resliced images under Reslice options and select Mean image only.
5. Next, add the slice timing correction module to your batch file - SPM Temporal Slice timing.
6. Complete the slice timing module:
   1. Select Data Session.
   2. Click Dependency in the bottom right corner.
   3. In the pop-up window, select the realigned time series that will be generated during realignment - Realign: estimate & reslice: realigned images (sess 1) and press OK.
   4. Select Number of slices 64.
   5. Select TR 7.
   6. Select TA 6.8906 or 7-(7/64).
   7. Select Slice order [64:-1:1].
   8. Select Reference slice 32 or 64/2.
7. Next, add the coregistration module to your batch file - SPM Spatial Coregister Coregister: estimate.
8. Complete the coregistration module:
   1. Select Reference image Dependency.
   2. In the pop-up window, select the mean image that will be generated during realignment - Realign: estimate & reslice: mean image and press OK.
   3. Select Source image.
   4. In the pop-up window, navigate to sub-01/anat/.
   5. Select the anatomical image - sub-01_T1w.nii and press Done.
9. Now add the segmentation module - SPM Spatial Segment.
10. Complete the segmentation module:
    1. Select Data Volumes Dependency.
    2. In the pop-up window, select the coregistered anatomical image Coregister: estimate: coregistered images and press OK.
    3. Select Save bias corrected Save bias corrected (Save INU corrected in newer SPM versions).
    4. Select Deformation fields Forward.
11. Add the normalisation module - SPM Spatial Normalise Normalise: write.
12. Complete the normalisation module:
    1. Select Data New: Subject.
    2. Select Deformation field Dependency.
    3. In the pop-up window, select the deformation field that will be generated during segmentation - Segment: forward deformations and press OK.
    4. Select Images to write.
    5. Click Dependency.
    6. In the pop-up window, select the realigned and slice time corrected data - Slice timing: slice timing corr. images (sess 1).
    7. Optional: Under Writing options, change Voxel sizes form [2 2 2] to [3 3 3]. This will write images at a resolution closer to that at which they were acquired.
13. Add the smoothing module - SPM Spatial Smooth.
14. Complete the smoothing module:
    1. Select Images to smooth Dependency.
    2. In the pop-up window, select the realigned, slice time corrected, and normalised time series - Normalise: write: normalised images (subj 1) and press OK.
    3. Select FWHM and change [8 8 8] to [6 6 6].
15. Now that all your preprocessing steps have been specified, save this batch - File Save batch and script and name it, e.g. preprocessing_batch.mat. Make sure you select Save batch and script not Save batch. This will be important for the next step.

You can now run this batch to execute all selected preprocessing steps for this subject by clicking or use it to create a matlab script to process data from multiple subjects.