Software Setup

The ISAS method primarily relies on MATLAB, SPM2, SPM ISAS scripts, and the Healthy Normals Database.

  1. Required Software
  2. Recommended Software

Required Software

ISAS runs on SPM, a software package designed for the analysis of brain imaging data sequences. In turn, SPM is built on top of the Matlab platform. Therefore, ISAS requires that Matlab and SPM are installed.

Matlab

    Matlab is a numerical computational software package available from the MathWorks website. The current version is MATLAB 7.1 Service Pack 3. It is available for commercial use for approximately US$2000 and US$100 for an academic license with a limited set of toolboxes.
    NOTE: Be sure to install all the latest updates available for your version of Matlab before performing an ISAS analysis.
    ISAS has been successfully tested with the following versions of Matlab:
    1. 6.1.0.450 (R12.1)
    2. 6.5.1.199709 (R13 SP1)
    3. 7.0.4.365 (R14 SP2)
      4. NOTE: Matlab 7 (SP2) has some trouble with the contrast manager. To workaround this problem enter feature('JavaFigures',0); at the prompt.
    ISAS has known issues with the following versions of Matlab:
    1. 6.5.0.180913a (R13)
      In particular, this version of Matlab produces ISAS results that are significantly different from the versions listed above (ie. incorrect number of significant clusters).

SPM

    SPM is software written by the Wellcome Department of Imaging Neuroscience at University College London to aid in the analysis of functional neuroimaging data. It is written using MATLAB and is distributed as free software.

  1. If you do not have SPM2 currently running, it is freely available as a MATLAB toolbox from the SPM site. In order to correctly run ISAS, SPM must be installed within your MATLAB folder in a separate directory (ie. ..\MATLAB6p1\spm2).
  2. To run SPM2, first start MATLAB. Navigate to File->Set Path and add the directory where SPM2 was installed to the path list (be sure to use the Add with Subfolders... option for adding the SPM2 directory). If you have previously installed another version of spm, make sure that the version of SPM that you wish to open (in this case SPM2) is at the top of the list of paths.
  3. Once the path is set, just type spm at the MATLAB prompt.
  4. Once SPM loads select the PET&SPECT from the popup menu. This should launch the SPM interface.

ISAS Scripts & Healthy Normal Database

  1. Download the script files we provide from our downloads page, which should be placed in your SPM directory.
  2. Download the pre-processed (realigned, spatially normalized, masked, smoothed) Healthy Normal images from Processed_HN_SPM2.zip and extract them to a convenient location on your hard drive. We recommend, and ISAS assumes, that you extract the scans to C:\ISAS\Healthy_Normals.
    NOTE: By default ISAS assumes that you will store the Healthy Normal scans in C:\ISAS\Healthy_Normals\ If you choose a different path, be sure to change the folderlocation variable on line 13 of the healthy_normals_location.m script file to reflect the new location you select.
  3. Alternatively, if you wish to manually pre-process the scans using different parameters, download the raw scans from Raw_HN_Analyze.zip. Then once you have processed them, place them in C:\ISAS\Healthy_Normals or an alternate directory that you select. Be sure to read the instructions that apply to the pre-processed Healthy Normals (above) to specify a location for the scans.
    4. NOTE: For the SPM analysis to work properly it is essential that the Healthy Normal scans are preprocessed exactly the same way as the ictal and interictal SPECT scans you plan to analyze. If you will do the preprocessing of the ictal and interical SPECT scans with the default parameters described here, then you should use the preprocessed Healthy Normal scans. You will only need to download the “raw” scans if you plan to preprocess your ictal and interictal SPECT scans as well as the Healthy Normal scans using different parameters from the defaults described here.

Recommended Software

The following software packages are recommended complements to ISAS.

ImageJ

  1. Download and install the ImageJ (Image Processing and Analysis in Java) software from the downloads section of the following site.
  2. Download the plugins "analyze reader" and "analyze writer" necessary for the analyze format from the ImageJ website. Save these in the ImageJ plugins directory.
  3. Start up the ImageJ program and navigate to Plugins->Shortcuts->Install Plugin... to create a shortcut so that the analyze reader and writer plugins will become new menu items.
  4. Put the analyze reader in the Import menu and set the command to Analyze.

RView

  1. RView is software intended for volume image registration/segmentation and display.
    "This software integrates a number of 3D/4D data display and fusion routines together with 3D rigid volume registration using Normalised Mutual information. It also contains many interactive volume segmentation and painting functions for structural data analysis." - Colin Studholme
  2. To download this package visit the following site.
  3. Installation instructions are available here

Software that Converts Scans to Analyze Format

For scans to be analyzed by SPM2 they must be in Analyze format; however, if you are starting with a different file format (ie. Dicom) then follow the steps below.

Analyze Format

If you are starting with scans that are not in Analyze format, there are a number of ways to convert them to the appropriate format, and this will vary somewhat depending on what scanner and reconstruction methods were used.

  1. Open your reconstructed SPECT image in RView to check the voxel dimensions.
  2. Go to Scan Info in RView and note the voxel size (you will need this value later)
  3. Open ImageJ and go to File > Import > Raw… and select your .psm file.
  4. Now you must enter some parameters so the image will open:
    Image type: 16 bit unsigned
    Width and Height: 128 (the matrix dimension)
    Offset to first image: 2048 (this is the header length)
    Number of Images: 128
    Gap b/w images: 0
    Leave the other boxes unchecked and click Ok.
  5. You should be able to view your picker image at this point. Go to Image->Rotate->Flip Horizontally so that converted images will be in the same orientation as the SPECT template.
  6. Go to File->Save As->Analyze and save your raw file into Analyze format (this should produce a .hdr and an .img file)
  7. The voxel dimensions of your new image have been set to the default value (which is 1). In order to change it to the appropriate value as determined in Step 2, you can edit the header using MRIcro. Initialize MRIcro, and Open the header file of the scan. On the top left, there is a header information box and the voxel sizes (mm) are listed for X, Y and Z. Change these values to the appropriate values obtained from RView.
  8. Click on the save header icon and replace your existing header with the corrected version.
  9. Display your new file in SPM to verify that it looks ok.


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