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Hi,

This is due to the use of sinc interpolation in applyxfm4D.
There is usually some ringing associated with sinc interpolation
near sharp boundaries.  If you do not wish to modify the sinc  
interpolation
then you can simply apply a single affine matrix to a 4D dataset
using flirt directly as:
   flirt -applyxfm -init example_func2standard.mat -ref standard -in $ 
{func_name} -out ${func_name}_2std -interp trilinear

or replace -interp trilinear with -interp sinc -sincwindow X - 
sincwidth Y
where X and Y can take various options - see the help for flirt.

Hope this helps.
All the best,
	Mark



On 1 Apr 2010, at 21:00, Alok Deshpande wrote:

> I am using applyxfm4d to register all the volumes in a single fMRI  
> file to a std brain template using the same affine 4x4 matrix.
>
> Following is the command I used:
>
> applyxfm4D ${analysisdirectory}/${subject}/${func_dir}/$ 
> {func_name}.nii.gz ${analysisdirectory}/${subject}/${reg_dir}/ 
> standard.nii.gz ${analysisdirectory}/${subject}/${func_dir}/$ 
> {func_name}_2std.nii.gz ${analysisdirectory}/${subject}/${reg_dir}/ 
> example_func2standard.mat -singlematrix
>
> I am getting some negative intensities in the output fMRI file. I  
> think it might be the problem with interpolation. Has anybody  
> experienced this before? I will appreciate any help.
>
> -- 
> Alok S. Deshpande
> Graduate Student
> Electrical & Computer Engineering Department
> University of Wisconsin Madison