Dmitry wrote:

> Thank you Tom! I do get a graphical interface screen and I do
> enter 250 for the FOV, as 25X25cm is the FOV of my images.
>
> I just found instructions on how to enter FOV into command line
> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/to3d.html)
> and this is the command I used:
>
> to3d -time:zt 124 1 1s seq+z -xFOV 250A-P -yFOV 250S-I -zFOV
> 90L-90R '3D:-1:0:256:256:1:filename'

This is almost certainly not what you wanted. 250A-P is the same as 250A to 250P, or a FOV of 500. That's pretty unlikely. You probably wanted 125A-P, for a FOV of 250.



>
> Anything else you could suggest?
>

Look at the voxel sizes from running the command
3dinfo -short
on your functional and structural scans. Are they correct? Do you know (for certain) what is 'correct'. I have seen MANY examples where a scan operator entered something wrong for a particiant so their scans differed from others. I know you are having problems reading in your DICOM files, but does the command dicom_hdr return anything useful vis a vis voxel size? Does your scan operator keep records of such things, or can they load the data on the scanner console to determine?
Tom