PetAnalysisProtocol - MRC CBU Imaging Wiki
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This page describes a standard statistical analysis of activation PET data from the WBIC. It assumes a directory structure that is standard for WBIC data, with the PET activation files in a directory:

[some directory] / [subject number] /p00/00/spm/

where [some directory] is some directory holding the data for one or more subjects, and [subject number] is a WBIC subject number. The PET activation images are called "emiss_0xx_tra.img" where "xx" is the scan number in the series, usually from 00 to 11.

  1. In an Xterm (or equivalent) window, move to the directory that you want to run your analysis from. (If you are having trouble moving around a Unix environment, go to the help with unix page ). It is a very good idea to create a new directory for each analysis you do. This is because SPM stores the results of each analysis in the directory you started SPM (or Matlab) from. So if you start SPM from a directory with existing analysis files, it will overwrite them with the files of your new analysis.

    (For information on how to automate some of the analysis steps in SPM96, see automating condition and covariates input )

    Run SPM. Choose "PET and SPECT" version.

    In the top left-hand window, choose "Statistics."

  1. You will then be asked: "Choose design type."

    • If there is only one subject, then you want to do a single subject design.
    • If there is more than one subject, then you should usually choose "multi-subject". Sometimes you will need more complex designs, with different groups etc; these designs are not covered here

    • If within each subject your conditions were repeated (e.g. you had four conditions, each repeated three times), then you want to choose "with replications."

    • Otherwise if each scan is a single condition in your experiment, you want to pick "different conditions."

    This guide will assume that you have chosen "multi-subject with replications" since that is the most common form of analysis. The format is virtually the same for each design type, though.

    (N.B. The data will probably be less noisy, and more accurate, if you covary out time and movement drift for the scans in the order they were given to each subject - see controlling for scan order and subject movement ).

  1. For "# of subjects" put in the number of subjects that you want to analyse.

  2. For "# of conditions" enter the number of different conditions you gave each subject.

  3. The SPMget dialog box will then open, asking you to choose the scans for the first subject and the first condition. Either type in the precise address for the directory of the .../p00/00/spm/snemiss files for the first subject in the blue slot at the top of this dialog box, or look for the closest match in the "Previous Directories" list below this, or navigate using the mouse in the main files list box (with the red names) by choosing ".." to move up one directory and clicking once on a directory name to enter into that directory. To the right of the "Filter:" button, there is another blue box. It will initially say "*.img" Once you are in the right directory for the first subject, change the wording of this blue box to "sn*.img" ("s" stands for "smoothed" and "n" stands for "normalised" - two preprocessing terms). In the main box below, only the 12 (or 6 or whatever) scans of subject 1 will be presented, each in the form of "snemiss_0**_tra.img" (assuming they are from the Wolfson). Click on the scans that correspond to the first condition. Remember that these scan numbers start at 000, rather than 1. Once all subject one, condition one scans have been highlighted, press "Done." You will then be prompted for subject one, condition two scans, etc. for all conditions for subject one, and then once this is completed, the same process will be needed for subject two. If your scans are roughly in the same place on the server, it might be easiest to change the subject number in the blue slot at the top to the new subject number, and press enter, to see all the snemiss*.img scans in the right place for the next subject. Repeat all these procedures until all conditions for all subjects have been chosen.

  1. The SPMget dialog box will close, and in the bottom left window, you will be asked to "select global normalisation." Choose: "AnCova {subject specific}.". For some explanation of the different types of global normalisation, as well as grand mean scaling and gray matter threshold (below), see the SPM statistics tutorial and associated matlab script

  2. You will then be asked to choose: "Grand Mean Scaling..." Pick "Scaling of Overall Grand Mean."
  3. You will then be asked "Value for Grand Mean?" Leave this at the default of 50. (The easiest way to choose SPM defaults is to click with the left hand mouse button somewhere else in the window and press Return.

  4. Next "Gray Matter threshold?" is requested. Again leave this at the default of 0.8.

  1. You will then be asked to choose your "# of contrasts." To find out what contrasts are and how to choose the contrast to reflect the condition comparison you want to run, see the page on simple contrasts explanation. When you have worked out on paper what contrasts you want to run, then enter the number of contrasts in the slot. You will then be asked for the details of contrast 1. Enter this in as specified above, and repeat for all the contrasts.

  2. Once this is finished, your input is completed, and after computation, the analysis will be complete and ready to view. You can review the default output in the file (see SPM tips and tricks ), or you can interrogate the results more extensively using SPM's graphical examination of results.

Daniel Bor 4/5/99

CbuImaging: PetAnalysisProtocol (last edited 2013-03-07 21:24:02 by localhost)