Enhanced MR Images Flipped

AFNI Message Board
1

Hi,

I’ve got some Enhanced MR images that are coming through flipped I-S after to3d.

I can fix the anatomic series by including the -oblique_origin flag. The fMRI and DTI series remain flipped even if I use that flag.

These are from a Siemens Vida 3T scanner. What is the best solution for using Enhanced MR formatted images with AFNI? Will changing the acquisition direction make a difference?

Many Thanks,
-Chad

2

So changing the acquisition direction seems to orient the images properly:


Per-frame Functional Groups Sequence 	(5200,9230) 
>Plane Position Sequence 	(0020,9113)
>>Image Position (Patient) 	(0020,0032) 	=	-96.313\-89.5543\-73.0048
>Plane Orientation Sequence 	(0020,9116)
>>Image Orientation (Patient) 	(0020,0037)  	=	1\0\0\0\1\0
>Pixel Measures Sequence 	(0028,9110)
>>Slice Thickness 	(0018,0050) 	 	 	=	2
>>Spacing Between Slices 	(0018,0088) 	=	2
>>Pixel Spacing 	(0028,0030) 	 	 	 	=	2.01923\2.01923
:
:
>Plane Position Sequence 	(0020,9113)
>>Image Position (Patient) 	(0020,0032) 	=	-96.313\-89.5543\-71.0048
>Plane Orientation Sequence 	(0020,9116)
>>Image Orientation (Patient) 	(0020,0037)  	=	1\0\0\0\1\0
>Pixel Measures Sequence 	(0028,9110)
>>Slice Thickness 	(0018,0050) 	 	 	=	2
>>Spacing Between Slices 	(0018,0088) 	=	2
>>Pixel Spacing 	(0028,0030) 	 	 	 	=	2.01923\2.01923
:
:

Results in a correct BRIK.

However, if the images are ordered S → I, the result is an upside down brain with incorrect DICOM coordinates. It appears AFNI is using the origin point from the first item in the Per-frame Functional Groups Sequence and assuming it is the most inferior slice (axially). This may be a serious issue for enhanced MR images collected sagittally.

I was able to correct using


3drefit -orient RAS raw+orig
3

Thanks for this information. We are interested in this problem and avoiding all kinds of flipped data. Please send me an example. I’ll PM you instructions. Have you tried dcm2niix_afni or dcm2niix to read the DICOM data?

4

I’ve uploaded the data.

dcm2niix does result in properly oriented images, but I’m hoping to3d will as well since it’s incorporated into a lot of our legacy scripts.

Thank You!
-Chad