BatchSmallVolumeCorrections - MRC CBU Imaging Wiki

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Type the odd letters out: scieNce GATHeRS knowledge fAster tHAN SOCIeTY GATHErS wisdom

Revision 1 as of 2010-01-05 18:01:57

location: BatchSmallVolumeCorrections

Batch processing of small volume corrections

The standard small volume correction function in SPM5 (spm_VOI) requires input from the GUI for certain parameters (e.g., the shape of the VOI), and hardcodes others (e.g., the number and spacing of maxima in the table). [attachment:spm_VOI_Custom.m This function] is a variant of the default spm_VOI that includes a struct for setting custom parameters.

The standard spm_VOI is called with table = spm_VOI(SPM, xSPM, hReg). spm_VOI_custom works exactly the same way, but also takes an optional third CustomParameters input. CustomParameters is a struct that contains any of up to 5 parameters. If the xyzmm, SPACE and D parameters are defined, extracting the results table for a VOI becomes fully automatic with no GUI input required.

To use this function, bring up some results in SPM (you can [wiki:SpmBatchPrintContrasts automate this process too]) to define the necessary SPM, xSPM and hReg inputs. Then, try something like:

% Produces the same output as spm_VOI or just using the small volume button in the GUI
T = spm_VOI_custom(SPM,xSPM,hReg);

% Now let's specify some custom settings
CustomParameters.Num = 8; % maxima per cluster (default 16)
CustomParameters.Dis = 8; % distance among maxima (mm, default 4)
CustomParameters.xyzmm = [10 -10 10]; % custom centre coordinates (mm)
CustomParameters.SPACE = 'S'; % Spherical VOI
CustomParameters.D = 15; % radius (mm) in the case of a spherical VOI

% This table should look quite different
T2 = spm_VOI_custom(SPM,xSPM,hReg,CustomParameters);

(JohanCarlin)