AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Chad N
January 21, 2020 02:56PM
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
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Subject Author Posted

Enhanced MR Images Flipped

Chad N January 16, 2020 11:38AM

Re: Enhanced MR Images Flipped

Chad N January 21, 2020 02:56PM

Re: Enhanced MR Images Flipped

Daniel Glen January 21, 2020 07:48PM

Re: Enhanced MR Images Flipped

Chad N January 27, 2020 11:07AM