Hi,

I have a compressed DICOM file of oblique images acquired with a Philips scanner that I'm trying to convert to afni format. It is only one file (IM_0002). The protocol parameters are:

Stacks = 1;
type = "parallel";
slices = 40;
slice gap = "user defined";
gap (mm) = 0.5;
slice orientation = "transverse";
fold-over direction = "AP";
fat shift direction = "P";
Stack Offc. AP (P=+mm) = -20.8249245;
RL (L=+mm) = 0;
FH (H=+mm) = 56.4826317;
Ang. AP (deg) = 0;
RL (deg) = 5.02629232;
FH (deg) = -0;
Free rotatable = "no";
Minimum number of packages = 1;
Slice scan order = "ascend";
TR = "user defined";
(ms) = 2000;
Dynamic study = "individual";
dyn scans = 300;
dyn scan times = "shortest";
fov time mode = "default";
dummy scans = 2;
immediate subtraction = "no";
fast next scan = "no";
synch. ext. device = "no";
dyn stabilization = "regular";
prospect. motion corr. = "no";
Total scan duration = "10:08.0";

So I used:

to3d -skip_outliers -epan -prefix baseline -time:zt 40 300 2000 alt+z IM_0002

(I had to use 300 timepts because 304 gave an error of wrong number of slices)

But this gave weird results. Only the axial view shows a brain (the sagittal and coronal views show grayscale values in a thin rectangular box). There are 40 slices in the axial view, but they are all the same. Only scrolling through the voxel timepoints for a given slice changes the slices. There are 300 timepts.

So there must be something wrong with the order that the images were acquired. I tried using -time:tz instead but this gave 300 axial slices with 40 timepts per voxel.

Any suggestions are very welcome. Thank you!