map.createvmp
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— | map.createvmp [2010/06/23 11:43] (current) – created jochen | ||
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+ | ====== map.CreateVMP ====== | ||
+ | ===== Motivation ===== | ||
+ | This method can be used to transfer a statistical map ([[xff - MAP format|MAP]]) from [[xff - FMR format|FMR]] space (where minimal smoothing is applied to the data) to the [[xff - VMP format|VMP format]] in normalized (ISO- / [[xff - VTC format|VTC]]) voxel space (and, potentially, | ||
+ | |||
+ | ===== Requirements ===== | ||
+ | You need: | ||
+ | |||
+ | * one (or multiple) [[xff - MAP format|MAP]] object(s) containing the statistical map(s) you wish to display on a [[xff - VMR format|VMR]] (or [[xff - SRF format|SRF]]) | ||
+ | * the initial alignment ([[xff - TRF format|IA.trf]]) and fine alignment ('' | ||
+ | * if you wish to visualize the data on either the '' | ||
+ | * further, if you wish to visualize this data on a surface (SRF), you also need the TAL-transformed SRF object | ||
+ | |||
+ | ===== Method reference (' | ||
+ | < | ||
+ | |||
+ | | ||
+ | |||
+ | Input fields: | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | .df degrees of freedom, 1x1 or 1x2 DF setting | ||
+ | |||
+ | | ||
+ | |||
+ | | ||
+ | |||
+ | ===== Input fields (details) ===== | ||
+ | ==== fmr ==== | ||
+ | The '' | ||
+ | |||
+ | This is required as the [[xff - MAP format|MAP]] object on which the method is called does **not** contain the required spatial information about resolution, etc.! | ||
+ | |||
+ | ==== afs ==== | ||
+ | This is a cell array with the required transformation ([[xff - TRF format|TRF]] and [[xff - TAL format|TAL]]) objects. For example, you could use the following lines of code to create one such array: | ||
+ | |||
+ | <code matlab map_createvmp_getafs.m> | ||
+ | ia = xff(' | ||
+ | if isempty(ia) || ... | ||
+ | | ||
+ | error(' | ||
+ | end | ||
+ | |||
+ | % request FA.trf | ||
+ | fa = xff(' | ||
+ | if isempty(fa) || ... | ||
+ | | ||
+ | error(' | ||
+ | end | ||
+ | |||
+ | % request ACPC.trf | ||
+ | acpc = xff(' | ||
+ | |||
+ | % request TAL.trf (if ACPC is not empty) | ||
+ | if ~isempty(acpc) | ||
+ | tal = xff(' | ||
+ | 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{: | ||
+ | |||
+ | ==== vmpfile ==== | ||
+ | Either leave blank of give desired output filename of [[xff - VMP format|VMP object]] to be created. | ||
+ | |||
+ | ==== meth ==== | ||
+ | Interpolation method to use. For maximum quality (lowest smoothing between MAP and VMP), set to ''' | ||
+ | |||
+ | ==== res ==== | ||
+ | Depending on the resolution in the '' | ||
+ | |||
+ | ==== bb ==== | ||
+ | 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 ''< | ||
+ | |||
+ | ==== o ==== | ||
+ | This is only to be used if the '' | ||
+ | |||
+ | ===== Complete syntax example ===== | ||
+ | This example assumes the '' | ||
+ | |||
+ | <code matlab map_createvmp_example> | ||
+ | % - 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, | ||
+ | vmp.SaveAs;</ |
map.createvmp.txt · Last modified: 2010/06/23 11:43 by jochen