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Spatial preprocessing

Display

Display eg. the first functional image using the Display button. Note orbitofrontal and inferior temporal drop-out and ghosting. This can be seen more clearly by selecting Brighten from the Effects menu in the Colours menu from the SPM Figure tab at the top of the Graphics window.

Signal dropout in EPI images.

Realignment

Under the spatial pre-processing section of the SPM base window select Realign (Est & Res) from the Realign pulldown menu. This will call up a realignment job specification in the batch editor window. Then

  • Highlight data, select New Session, then highlight the newly created Session option.

  • Select Specify Files and use the SPM file selector to choose all of your functional images eg. sM03953_0005_*.img. You should select 351 files.

  • Save the job file as eg. DIR/jobs/realign.mat.

  • Press the Run button in the batch editor window (green triangle).

This will run the realign job which will write realigned images into the directory where the functional images are. These new images will be prefixed with the letter “r”. SPM will then plot the estimated time series of translations and rotations. These data, the realignment parameters, are also saved to a file eg. rp_sM03953_0005_0006.txt, so that these variables can be used as regressors when fitting GLMs. This allows movements effects to be discounted when looking for brain activations.

SPM will also create a mean image eg. meansM03953_0005_0006.{hdr,img} which will be used in the next step of spatial processing - coregistration.

Realignment of face data: Movement less than the size of a voxel, which for this data set is 3mm, is not considered problematic.

Slice timing correction

Press the Slice timing button. This will call up the specification of a slice timing job in the batch editor window. Note that these data consist of N=24 axial slices acquired continuously with a TR=2s (ie TA = TR - TR/N, where TA is the time between the onset of the first and last slice of one volume, and the TR is the time between the onset of the first slice of one volume and the first slice of next volume) and in a descending order (ie, most superior slice was sampled first). The data however are ordered within the file such that the first slice (slice number 1) is the most inferior slice, making the slice acquisition order [24 23 22 ... 1].

  • Highlight Data and select New Sessions

  • Highlight the newly create Sessions option, Specify Files and select the 351 realigned functional images using the filter ^r.*.

  • Select Number of Slices and enter 24.

  • Select TR and enter 2.

  • Select TA and enter 1.92 (or 2 - 2/24).

  • Select Slice order and enter 24:-1:1.

  • Select Reference Slice, and enter 12.

  • Save the job as slice_timing.mat and press the Run button.

SPM will write slice-time corrected files with the prefix a in the functional data directory.

Coregistration

Select Coregister (Estimate) from the Coregister pulldown menu. This will call up the specification of a coregistration job in the batch editor window.

  • Highlight Reference Image and then select the mean functional image meansM03953_0005_0006.img.

  • Highlight Source Image and then select the structural image eg. sM03953_0007.img.

  • Press the Save button and save the job as coreg.job

  • Then press the Run button.

SPM will then implement a coregistration between the structural and functional data that maximises the mutual information. The image displayed below should then appear in the Graphics window. SPM will have changed the header of the source file which in this case is the structural image sM03953_0007.hdr.

Mutual Information Coregistration of Face data.

Segmentation

Press the Segment button. This will call up the specification of a segmentation job in the batch editor window. Highlight the Volumes field in Data > Channels and then select the subjects coregistered anatomical image eg. sM03953_0007.img. Change Save Bias Corrected so that it contains Save Bias Corrected instead of Save Nothing. At the bottom of the list, select Forward in Deformation Fields. Save the job file as segment.mat and then press the Run button. SPM will segment the structural image using the default tissue probability maps as priors. SPM will create, by default, gray and white matter images and bias-field corrected structural image. These can be viewed using the CheckReg facility as described in the previous section 1.

Grey matter (top) produced by segmentation of structural image (below).

SPM will also write a spatial normalisation deformation field file eg. y_sM03953_0007.nii file in the original structural directory. This will be used in the next section to normalise the functional data.

Normalise

Select Normalise (Write) from the Normalise pulldown menu. This will call up the specification of a normalise job in the batch editor window.

  • Highlight Data, select New Subject.

  • Open Subject, highlight Deformation field and select the y_sM03953_0007.nii file that you created in the previous section.

  • Highlight Images to write and select all of the slice-time corrected, realigned functional images arsM*.img. Note: This can be done efficiently by changing the filter in the SPM file selector to ^ar.*. You can then right click over the listed files, choose Select all. You might also want to select the mean functional image created during realignment (which would not be affected by slice-time correction), i.e, the meansM03953_0005_006.img. Then press Done.

  • Open Writing Options, and change Voxel sizes from [2 2 2] to [3 3 3]2.

  • Press Save, save the job as normalise.mat and then press the Run button.

SPM will then write spatially normalised files to the functional data directory. These files have the prefix w.

If you wish to superimpose a subject’s functional activations on their own anatomy 3 you will also need to apply the spatial normalisation parameters to their (bias-corrected) anatomical image. To do this

  • Select Normalise (Write), highlight Data, select New Subject.

  • Highlight Deformation field, select the y_sM03953_0007.nii file that you created in the previous section, press Done.

  • Highlight Images to Write, select the bias-corrected structural eg. msM03953_0007.nii, press Done.

  • Open Writing Options, select voxel sizes and change the default [2 2 2] to [1 1 1] which better matches the original resolution of the images [1 1 1.5].

  • Save the job as norm_struct.mat and press Run button.

Smoothing

Press the Smooth button 4. This will call up the specification of a smooth job in the batch editor window.

  • Select Images to Smooth and then select the spatially normalised files created in the last section eg. war*.img.

  • Save the job as smooth.mat and press Run button.

This will smooth the data by (the default) 8mm in each direction, the default smoothing kernel width.

Functional image (top) and 8mm-smoothed functional image (bottom). These images were plotted using SPM’s "CheckReg" facility.

  1. Segmentation can sometimes fail if the source (structural) image is not close in orientation to the MNI templates. It is generally advisable to manually orient the structural to match the template (ie MNI space) as close as possible by using the “Display” button, adjusting x/y/z/pitch/roll/yaw, and then pressing the “Reorient” button. ↩

  2. This step is not strictly necessary. It will write images out at a resolution closer to that at which they were acquired. This will speed up subsequent analysis and is necessary, for example, to make Bayesian fMRI analysis computationally efficient. ↩

  3. Beginners may wish to skip this step, and instead just superimpose functional activations on an “canonical structural image”. ↩

  4. The smoothing step is unnecessary if you are only interested in Bayesian analysis of your functional data. ↩