Dear all:

Recently I am troubled by the first pilot images that I got from the philips 1.5 T scanner. As the first pilot, I tried to3d on the functional data, and realized that I have to do some x y orientation changes in order to make them 'looked' right. And then when I tried to generate the SPGR dataset, the to3d output messages as below:

++ to3d: AFNI version=AFNI_2008_07_18_1710 (Sep 30 2008) [32-bit]
++ Authored by: RW Cox
++ Counting images: total=128 2D slices
++ DICOM WARNING: file T1_3D0001.dcm has Rescale tags; setenv AFNI_DICOM_RESCALE YES to enforce them
++ DICOM WARNING: Slice_Spacing=1.000000 smaller than Slice_Thickness=2.000000

++ Setting environment variable AFNI_SLICE_SPACING_IS_GAP ++
++ to YES will make the center-to-center slice distance ++
++ be set to Slice_Spacing+Slice_Thickness= 3.000. ++
++ This is against the DICOM standard [attribute (0018,0088) ++
++ is defined as the center-to-center spacing between slices, ++
++ NOT as the edge-to-edge gap between slices], but it seems ++
++ to be necessary for some GE scanners. ++
++ ++
++ This correction has been made on this data: dz= 3.000. ++
++ ++
++ Setting AFNI_SLICE_SPACING_IS_GAP to NO means that the ++
++ DICOM Slice_Spacing variable will be used for dz, replacing ++
++ the Slice_Thickness variable. This usage may be required ++
++ for some pulse sequences on Phillips scanners. ++

++ DICOM WARNING: Slice_Spacing=1.000000 smaller than Slice_Thickness=2.000000
++ Each 2D slice is 288 X 288 pixels
++ Voxel dimensions: 0.9028 X 0.9028 X 3.0000 mm
++ Image data type = short
++ Reading images: ++ DICOM WARNING: file T1_3D0002.dcm has Rescale tags; setenv AFNI_DICOM_RESCALE YES to enforce them
++ DICOM WARNING: no more Slice_Spacing messages will be printed
++ DICOM WARNING: no more Rescale tags messages will be printed
................................


and when I opened the AFNI to look at the images of 3 viewpoints, only the axial one looked ok, the sagittal and coronal ones were scaled differently. I looked through the forum and tried

AFNI_DICOM_WINDOW = YES // YES==use DICOM rescale tags
AFNI_DICOM_WINDOW = NO // YES==use DICOM window tags

but it didn't help.

The worse problem was that because I've changed the orientations of the functional data to make them look right, the different scale seems to make the coregistration impossible (because now the scale of two images are totally off).

any suggestions?
thanks, chun-chia

p.s. For better explanation, I put the views on here:
[myweb.ncku.edu.tw]

As can be seen, the anat files are stretched on sagital and coronal views, making the anat and epi incompatible for coregistration.