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.
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Alok S. Deshpande
Graduate Student
Electrical & Computer Engineering Department
University of Wisconsin Madison
