Producing Tables of Coordinates (SPM)
Most neuroimaging papers include a section in the results describing some statistical comparison (or contrast) between two or more conditions (one of those conditions might be an implicit baseline). This is probably what comes to mind when you think of presentations of fMRI research showing what I refer to as "blobs of activation", and what people are generally referring to when they say that some part of the brain "lights up" when doing some task.
Along with figures showing beautiful renderings of these statistical comparisons, the presentation of these findings should also include a tabular summary of these data because a 2D rendering of 3D data loses much precision. Numerical data may also later be entered into a meta-analysis, whereas a figure cannot. The procedure below describes how to generate the table of coordinates that should accompany the figure produced by following the wiki entry for producing a contrast rendering.
Obtaining the SPM Table of Coordinates
'Note that the table of coordinates should be produced using identical parameters to those used to produce the brain renderings. This is most easily done by producing the table and the 3D contrast volume at the same time.'
In SPM, load the contrast of interest
- Select Results from the GUI interface
- Identify the SPM.mat file of interest. For a group-level contrast (the typical case), there should be an SPM.mat file in the directory designated to receive the Random Effects analysis results
- Select the contrast of interest
- Assign the desired uncorrected (or FWE corrected) significance threshold and extent threshold (if any; the default extent threshold value is 0)
- FILL OUT THE REST-- I CAN'T REMEMBER THE EXACT BUTTON NAMES
You can (and should) save the SPM output to a postscript (.ps) file at this point. The .ps file can be opened in Adobe Acrobat Reader.
Generating the Table of Coordinates for a Manuscript
A properly formatted table of coordinates should have the following structure:
| Region (BA) | Size | SIG | Max Z | x | y | z |
|---|---|---|---|---|---|---|
| Table data here | ||||||
| Note: L, left; R, right; BA, Brodmann Area; Size, cluster size measured in voxels (or mm^3); FDR, FDR-corrected significance level (used for SIG column; alternatively, FWE, Family-wise error corrected significance level); Max Z, maximum Z statistic reported for cluster. Coordinates reflect standard MNI space | ||||||
This table simply follows the APA 6th Edition guidelines for table presentation. There are solid horizontal lines marking the bottom of the table data, and at the top and bottom of the header row. No horizontal lines separate rows within the table data, nor are there vertical column lines. Table notes appear immediately below the table. I generally accomplish this by adding a borderless "hidden" row after the last row of table data, spanning all table columns (you might use Merge Cells to do this in MS Word).
Sample Table
| Region (BA) | Size | FDR | Max Z | x | y | z |
|---|---|---|---|---|---|---|
| R. Superior Temporal Gyrus (BA 21) | 861 | < 0.001 | 6.58 | 63 | -27 | 3 |
| L. Superior Temporal Gyrus (BA 48/21) | 1009 | < 0.001 | 6.09 | -57 | -9 | -3 |
| Note: L, left; R, right; BA, Brodmann Area; Size, cluster size measured in voxels '; FDR, FDR-corrected significance level ; Max Z, maximum Z statistic reported for cluster. Coordinates reflect standard MNI space | ||||||
If you have many occurrences of the same anatomical region, you might use standard abbreviations (e.g., STG: Superior Temporal Gyrus; IFG: Inferior Frontal Gyrus) to make your tables more compact. Abbreviations should be listed in the table notes.