PE direction on a GE scanner will depend upon whether you scanned in clinical or research mode (default PE direction is different in each mode), and which OS the scanner used (eg. Older HD versions or newer DV versions).

If you assume the first dataset is A-P and the second (blipped) is P-A, then run topup with
0 -1 0 0.1
0 1 0 0.1

If the areas of inhomogeneity on the field map output (my_fout) are black, then the first dataset is P-A and the blipped is A-P. Confirm this by running 
0 1 0 0.1
0 -1 0 0.1
The my_fout should show the temporal bone region as white.

Jesper please correct me if I am wrong!

Jerome


On Thu, 12 Sep 2019, 22:15 Jesper Andersson, <[log in to unmask]> wrote:
Dear Ariadna,

are you saying the two images are very similar? Can you do a screen grab of the slice that shows the maximum difference between the two images and email me (outside of the mailbase)?

Jesper

On 12 Sep 2019, at 13:39, Ariadna Albajara Sáenz <[log in to unmask]> wrote:

Dear Jesper, 

Thank you for your answer. 
Unfortunately in my images this is not evident at all. Is there another way to check this? 
Thank you in advance, 
Ariadna
Ariadna Albajara Sáenz
UR2NF - Neuropsychology and Functional Imaging Research Group
CRCN - Center for Research in Cognition and Neurosciences
       
UNIVERSITÉ LIBRE DE BRUXELLES, Avenue F. Roosevelt 50, CP 151, 1050 Brussels (Belgium). 
Office: DB10-237


El jue., 12 sept. 2019 a las 13:09, Jesper Andersson (<[log in to unmask]>) escribió:
Dear Ariadna,

probably the easiest way of figuring this out is to go to


and compare the images you see there with your own.

Jesper

On 12 Sep 2019, at 11:55, Ariadna Albajara Saenz <[log in to unmask]> wrote:

Dear all,
I have two DTI acquisitions (acquired with GE and "InPlanePhaseEncodingDirectionDICOM": "COL"):

1- one for which: "PhaseEncodingDirection": "j"
2- a second acquisition (phase-shift) for which "PhaseEncodingDirection": "j-"

Could someone tell me with this information which one corresponds to anterior ->posterior and which one to posterior -->anterior?

Thank you in advance,

Ariadna

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