Dmitry wrote:

> Thanks, Tom, for your answer.
>
> The datasets do not overlay properly, even in the +orig view. >

This is certainly a problem. The two must overlap correctly in the orig view in order for the tlrc step to work. In original view, does the EPI data look 'bigger' than the structural?

> All anatomical and functional files are in the same folder. I
> run the to3d command like this:
>
> to3d -time:zt 124 1 1s seq+z '3D:-1:0:256:256:1:filename'
>
> You were saying "THE MOST LIKELY PROBLEM IS THAT VOXEL
> DIMENSIONS OR FOV WERE MISENTERED AT THE TO3D STEP." Is there
> something I'm missing in the above command line to distinguish
> the FOV?

Yes, there is something missing - a FOV When you use the 3D: options with to3d, it reads in the binary data only, no position or size info. I see from your other thread that you are having problems reading in DICOM files which has this info and would normally include the position data automatically. The command you ran should have brought up a graphical interface to enter your position/size info. You need to find that correct info and enter it. Note that it is fairly common to acquire structural and EPI scans at different FOVs. For example, we do our MPRAGES at a FOV of 256 to get 1mm voxels when imaging 256X256, and our EPIs with a FOV of 220 instead of 256 to get better inplane resolution at a 64x64 matrix.
Tom