Hi Daniel-

I suspect that I'm missing somethiing pretty easy here, so I've attached the to3d command i tried, along with the output, and the jpg images of the functional and anatomical slices so that you can see what is happening. Following this, I tried other commands from the help site (sorry I didn't save them then) but nothing changed what I was seeing. Since I can't recreate exactly what commands were previously tried, but if you don't mind, I'll just send this for now. I have updated to the most recent AFNI version and have the same problem. If it helps to see the original data, I had downloaded it to the AFNI site under my name on the 23rd.



to3d 2008_10_15_RM.MR.FINGER_FMRI.10.*

command line output:

++ to3d: AFNI version=AFNI_2008_07_18_1710 (Oct 21 2008) [32-bit]
++ Authored by: RW Cox
++ Counting images: total=4446 2D slices
++ DICOM NOTICE: 7x7 Siemens Mosaic of 39 128x108 images in file 2008_10_15_RM.MR.FINGER_FMRI.5.100.2008.10.15.11.02.38.703125.6899328.IMA
++ Data detected to be oblique
++ Each 2D slice is 128 X 108 pixels
++ Voxel dimensions: 1.9531 X 1.9531 X 2.5000 mm
++ Image data type = short
++ Reading images: ++ DICOM NOTICE: 7x7 Siemens Mosaic of 39 128x108 images in file 2008_10_15_RM.MR.FINGER_FMRI.5.101.2008.10.15.11.02.38.703125.6899346.IMA
++ DICOM NOTICE: no more Siemens Mosaic messages will be printed
..........................................
++ Slice based center matches mosaic center
Mosaic Center: -2.90558 -17.4334 -26.8765
Origin Coordinates: -126.929 -131.678 -37.9687
++ Making widgets.....

The image parameters for each run were: functional: 114 volumes collected, TR 3000ms, TE 43ms, slice thickness 2.5mm, axial aqusition, inf to superior, interleved, on the Siemens 3T scanner. For the anatomical, the slice thickness was 1mm (resolution should be 1 x 1 x 1 mm).
Many thanks for any help,
Elizabeth