After starting VOI Tool utility the following window will appear
Creating one or more VOIs on the basis of SPM clusters. After clicking this button the "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. After this "Select clusters" dialog box will appear with the list of all available SPM clusters. Name of each cluster is the string "NAME N X Y Z", where NAME is "title for comparison" selected in SPM99 contrast manager, N is the number of voxels in the cluster, and X Y Z - coordinates of local maximum in the cluster. To select more than one cluster use CTRL and/or SHIFT clicking. Then for each selected cluster the VOI will be created and saved into the file VOINAME.voi in the current MATLAB directory, where VOINAME - name of the VOI as listed in the "Select clusters" dialog box. If file with this name already exists, user will be prompted to select new file to save VOI.
Creating VOI as thresholded image. After clicking this button user will be prompted to select *.img file from which VOI will be created. Then "Threshold input" dialog will appear and user should set threshold value. All image voxels with values greater or equal to this threshold value will be included in VOI. Then sequentially two progress bars "Read image data. Please wait" and "Set VOI data. Please wait" will appear and VOI will be created and saved into the file VOINAME.voi, where VOINAME name of the selected *.img file. This file will be created in the same directory where *.img was selected.
Creating box shaped VOI. After clicking this button "Create BOX shaped VOI (in mm)" dialog will appear and user should select VOI parameters. After setting parameters box shaped VOI will be created and saved into the file Box X Y Z.voi in the current MATLAB directory, where X Y Z are center coordinates in mm. If the file with this name already exists, user will be prompted to select new file to save VOI. Values X Y Z in file name may differ from those set by user because of before creating VOI center coordinates are rounded to multiples of corresponding voxel sizes.
These options allow to perform simple operations on existing VOIs. After this button dialog for selecting operands will appear and user should set both operands (select existing *.voi files). Then clicking on "Calculate" button starts new VOI creation and "Calculating. Please wait" progress bar will appear. After finishing calculations VOI will be saves into the file Operation.voi in the current MATLAB directory, where Operation is Union, Intersection, or Difference. If the file with this name already exists, user will be prompted to select new file to save VOI.
This option allow extract signal intensity data for given set of VOIs. Because signal intensity data are extracted from the Y.mad file the following note (see Tools for Functionally Defined Regions of Interests) should be made:
Caution. Y.mad file file needs to exist. Furthermore, the average VOI intensity will be based only on those voxels available in the Y.mad file. For this, it is best to set the SPM defaults so that the F threshold for fMRI_UFp variable is fMRI_UFp=1. In this way data from all voxels will available. (These changes need to be done before estimating the statistics).
After clicking this button the "Select SPM.mat" dialog from SPM99 will appear and user should select the SPM.mat file with results of the SPM99 statistical analysis. After selecting SPM.mat file "SPMget" dialog from SPM99 will appear and user should select VOI files for which data will be extracted. After selecting VOIs progress bar "Checking available data. Please wait..." will appear. At this time program is checking how much voxels are missed in Y.mad file for each VOI. If some data are missed the dialog with list of all VOIs will appear, in which for every VOI number of voxels with missed data, as well as the total number of voxels in VOI is shown. On the basis of this information user can select VOI for which data will be extracted. If no data are missed the above dialog will not appear and immediately another progress bar "Calculating VOIs average value. Please wait..." will appear. After finishing calculating user will be prompted to select file to save extracted data.
This option used to save extracted signal intensity data for given set of VOIs as plain ASCII test files (see Text signal intensity data) which can be used for further analysis with other statistical software. After clicking this button user will be prompted to select *.vda file with extracted data. After selecting file user will be prompted to select file name to save data. The selected file name will be used as the part of the file names for five text files containing different parts of information (see Text signal intensity data). Caution. Existing text files will be overwritten without prompting.