ConvertFuncToAMR Method


Description

Converts the first functional volume of an FMR project into an AMR file.

Syntax

objDocument.ConvertFuncToAMR(strAMRFileName)

Remarks

Valid only if objDocument is of type FMR. This method is useful to produce a "pseudo-anatomical" representation within the same space as the functional data. When short TR's are used (i.e. in event-related paradigms), the first measurement of the functional slices produces images with high T1-saturation, i.e. high signal level and good tissue contrast. The high signal drops rapidly with further measurements reaching a steady state. Since this signal change presents a problem for showing and analyzing time series data, the first few measurements are normally not read in when creating an FMR project. Because of good tissue contrast, It is, however, desirable to use the very first measurement as the images on which statistical maps should be shown. This is where the present method is useful: create an FMR project of the first volume only, then apply the method to produce a respective AMR file which can then be linked to the "real" FMR file containing the full time series data (except the very first measurements). Another advantage of using a pseudo-AMR file is that spatial smoothing does not change the AMR so that the anatomical location of functional clusters can be better visualized.
Another possibility to obtain a pseudo-AMR file would be to create an AMR project from the images of the first functional volume. Although this is possible, the presented method is recommended since it produces an FMR file which can be transformed to a VTC file of the first volume. This again can be used in stereotactic space to show statistical maps not only on T1-weighted data sets but also on the original EPI data.
The method corresponds to the function invoked by the Options->Convert func to AMR menu item. The transformation uses all default settings of the Rescale Images dialog which appears in the GUI version: the AMR will transform the original FMR slices (of the first volume) to a resolution of 256 x 256, it uses bilinear interpolation, it does not invert the intensity values and it does not invert the background. A method which allows to specify these settings will be provided shortly (ConvertFuncToAMREx).

Example

' VBScript
Set doc_firstvol = BrainVoyager.
OpenDocument("first_vol.fmr")
doc_firstvol.
ConvertFuncToAMR "func_as_anat.amr"
Set doc = BrainVoyager.
OpenDocument("cg_objects.fmr")
doc.
LinkAMRFile "func_as_anat.amr"
doc.
Save

// JScript
doc_firstvol = BrainVoyager.
OpenDocument("first_vol.fmr");
doc_firstvol.
ConvertFuncToAMR("func_as_anat.amr");
doc = BrainVoyager.
OpenDocument("cg_objects.fmr");
doc.
LinkAMRFile("func_as_anat.amr");
doc.
Save();

# PerlScript
$doc_firstvol = $BrainVoyager->
OpenDocument("first_vol.fmr");
$doc_firstvol->
ConvertFuncToAMR("func_as_anat.amr");
$doc = $BrainVoyager->
OpenDocument("cg_objects.fmr");
$doc->
LinkAMRFile("func_as_anat.amr");
$doc->
Save();