Hi there,

I have a subject, for a valid reason, whose scans have to be done in oblique instead of typical axial. And here are the coord. for the structural and functional scans.

structural:
First slice: R6.5, A26.9, I85.4
Final slice: R6.5, P22.2, S79.7

functional:
First slice: R6.5, P21.8, S54.1
Final slice: R6.5, A18.3, I74.8

Oblique angle: 287 (17 degrees from horizonal)

If they were scanned in axial, the second column(anterior-posterior) should be the same between the first slice and the final slice.

My problem is that I cannot think of a way to properly reformat my raw data (GE for anat. and spiral P files for func.) into .HEAD and .BRIK files.

For example, to do the reformatting, I would use the commands below.

structural:
> to3d -anat -skip_outliers -session ../afdir/ -prefix 3dvol -xFOV 116.5R-103.5L -yFOV ###P-###A -zSLAB ###I-###S ‘I.???’

functional:
> count -digits 3 -root 3D:0:0:64:64:1:P123456.7. 1 9490 | to3d -epan -session ../afdir -prefix run1 –anatparent ../afdir/3dvol+orig -xFOV 106.5R-93.5L -yFOV ###A-###P -zSLAB ###S-###I -time:tz 177 28 2000 seq+z -@

### represents the entries that I am not sure about.

I believe that 3drotate and imrotate and rotobrick are some of the methods to deal with oblique scans.

But my problem is that I am not too sure how to ceate a .HEAD and .BRIK files from my raw data in the first place (like what numbers should be in those ### entries), it's difficult for me to proceed further.

Thanks very much for your help. I really appreciate for your kind assistance.

Ricky