Running MNI Space utility

Running

Start Talairach Space utility typing MSU in MATLAB command window. Immediately "Select SPM.mat" dialog from SPM99 will appear and user should select the SPM.mat file with results of the SPM99 statistical analysis. After selection of the SPM.mat file user should answer the standard for SPM99 sequence of questions: "Select contrasts..." dialog, masking, title for comparison, height and extent thresholds. If there are no voxels above height threshold the warning "No voxels survive height threshold" will appear and utility will terminate. Otherwise user will be prompted to select file to save report. After selecting file progress bar "Processing. Please wait..." will appear. After finishing calculation report will be generated and saved in selected file and utility will terminated.

Output report format

In this section default format of the output report will be described. Output report is a plain ASCII text file, which consists of the title line, followed separate report for each cluster.

Report title is:

• Contrast name: "name",

where "name" is "title for comparison" set in SPM99 dialog.

Cluster report consists of the two lines title and the reports for level 1, level 2, etc. regions, separated by underscore line.

Cluster report title is

• Number of Voxels N
• Max. coordinates x y z

where N is the number of voxels in the cluster, x, y, z - coordinates of the primary maximum of the cluster.

Level K (K =1,...,5) report includes one line for every region of the level K, which have nonempty intersection with the cluster under consideration. This line consists of the region name and two numbers. First number is the ratio of the intersection volume to cluster volume, second - ratio of the intersection volume to region volume. Note that volumes (defined as product of the number of voxels on the voxel volume) are used to calculate ratio, because of voxel sizes may be different for regions (fixed size 2x2x2x mm) and clusters (arbitrary, set in SPM analysis).

Editing output format

In the previous section default format of the output report was described. This format can be modified by editing plain ASCII file ihb_MniSpaceOptions.m. There are two ways of modification:

1. Into cluster report can be included only those regions for which intersection with cluster is greater than given value N in percents. To make such modification line "Threshold, 0" should be changed to the line "Threshold, N".
2. Some levels can be excluded from the cluster report. For example, to exclude level 2 regions line "Show level 2 labels,1" should be changed to "Show level 2 labels,0".