map.CreateVMP

This method can be used to transfer a statistical map (MAP) from FMR space (where minimal smoothing is applied to the data) to the VMP format in normalized (ISO- / VTC) voxel space (and, potentially, from there to SMP format in surface space) in BrainVoyager QX.

You need:

• one (or multiple) MAP object(s) containing the statistical map(s) you wish to display on a VMR (or SRF)
• the initial alignment (IA.trf) and fine alignment (FA.trf) files
• if you wish to visualize the data on either the ACPC.vmr or the TAL.vmr, you also need the ACPC.trf and ACPC.tal files
• further, if you wish to visualize this data on a surface (SRF), you also need the TAL-transformed SRF object

 MAP::CreateVMP  - create VMP from FMR based MAP object
 
 FORMAT:       vmp = map.CreateVMP(fmr, afs [, vmpfile, meth, res, bb, o])
 
 Input fields:
 
       fmr         FMR object matching MAP
       afs         cell array with alignment files, {ia, fa, acpc, tal}
       vmpfile     target VMP filename, if not given: unsaved
       meth        interpolation, 'nearest', {'linear'}, 'cubic'
       res         VMP resolution, default: 1
       bb          bounding box, default: small TAL box
       o           optional struct with settings
        .df        degrees of freedom, 1x1 or 1x2 DF setting
 
 Output fields:
 
       vmp         resulting VMP object

The fmr input variable must be a valid FMR object, e.g. you can use the file selector of xff by using the syntax, fmr = xff('*.fmr');.

This is required as the MAP object on which the method is called does not contain the required spatial information about resolution, etc.!

This is a cell array with the required transformation (TRF and TAL) objects. For example, you could use the following lines of code to create one such array:

map_createvmp_getafs.m

% request IA.trf
ia = xff('*IA*.trf', 'Please select IA TRF file...');
if isempty(ia) || ...
   ~isxff(ia, 'trf')
    error('No IA TRF file selected.');
end
 
% request FA.trf
fa = xff('*FA*.trf', 'Please select FA TRF file...');
if isempty(fa) || ...
   ~isxff(fa, 'trf')
    error('No FA TRF file selected.');
end
 
% request ACPC.trf
acpc = xff('*ACPC*.trf', 'Please select ACPC file... (leave blank for ISO-voxel space)');
 
% request TAL.trf (if ACPC is not empty)
if ~isempty(acpc)
    tal = xff('*.TAL', 'Please select TAL file...');
end
 
% compile afs cell array
if ~isempty(acpc)
    if ~isempty(tal)
        acpc = {acpc, tal};
    else
        acpc = {acpc};
    end
else
    acpc = {};
end
afs = {ia, fa, acpc{:}};

Either leave blank of give desired output filename of VMP object to be created.

Interpolation method to use. For maximum quality (lowest smoothing between MAP and VMP), set to 'cubic' (or even 'lanczos3').

Depending on the resolution in the FMR (and MAP), as well as the purpose for display (e.g. surface space), you might want to select an appropriate resolution. Eventually, using 1 (the default) will only cost performance during VMP creation and some additional disk space while ensuring that any additional interpolation (from VMP to SMP) does not introduce further smoothing.

Bounding box to be used. This must be given in BrainVoyager coordinate system (TAL axes order, however). For instance, the default bounding box is given as [59, 57, 52; 197, 231, 172], which means that the X axis will be covered from 59 to 197 (in .res step size), which translates to TAL coordinates 69 through -69 (BrainVoyager's X axis runs into negative TAL X axis direction!) and so forth.

This is only to be used if the MAP object does not contain the correct degrees of freedom (DF1/DF2) parameter. To override the settings in the MAP (e.g. the statistic therein is an F-map), use the following syntax: o = struct('df', [3, 140]); for (3, 140) being the DF.

This example assumes the afs argument has been made already (see above!):

map_createvmp_example

% the following variables are being used and must exist
% - map: MAP object (fitting FMR!)
% - fmr: FMR object
% - afs: collection of TRF/TAL objects
% the following settings are used
% - no VMP filename (requires manual saving)
% - high quality interpolation (lanczos3)
% - 1mm resolution (best for going to SRF/SMP later)
% - large bounding box (covering ALL TAL space)
% - no df override
vmp = map.CreateVMP(fmr, afs, '', 'lanczos3', 1, [44, 44, 38; 212, 242, 194]);
vmp.SaveAs;