Hi
Regarding Philips scanners, I would like to add a question to this thread:
As I understand it, the question of knowing A>>P or A<<P is less important as you can try -1 or +1 and see which actually improves the distortions and then use that in FSL. However, as I need to use T2-images as the second B0-image, I understand it to be that
one needs to get the read out time correct for the actual B0-image (not as necessary when using two inverse B0 with the same readout time). Can the formula for read out time shown at FSL/eddy/faq be considered to be accurate in cases of Philips as well?
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq#How_do_I_know_what_to_put_into_my_--acqp_file
Also, is it possible to retrieve the information needed to calculate the read out time from the DICOM or nifty-images? I am quite sure I know the EPI factor, but less sure of the echo spacing.
Any help much appreciated.
Best,
nick
Niklas Lenfeldt, PhD, MSc, MAJ SWE A
Clinical Neuroscience, Umeå university
Phone: +46 70 609 66 87
Email:
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Från: FSL - FMRIB's Software Library [
mailto:[log in to unmask]] För Andreas Bartsch
Skickat: den 11 februari 2015 10:42
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Ämne: Re: [FSL] Acquisition parameters Philips dti data
Hi,
you sould be able to tell by the direction of the geometric distortions.
For A>P, these should run from anterior to posterior.
Cheers,
Andreas
Am 11.02.15 10:27 schrieb "M Barendse" unter <
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Dear FSL users,
We have acquired DWI data with a Philips 3T scanner. I would like to
run topup and eddy on these and for that you need to create a file with
acquisition parameters. However it¹s unclear to me what to put in this
file.
Philips scanners do not give you the phase encoding direction. Instead,
it gives a 똣old-over direction¹ and 똣at shift direction¹. Our scans are
all in 똣old-over direction = ³AP²¹, and we have 1 b0 and 30 dwi¹s with
똣at shift direction = ³A² as well as 1 b0 and 30 dwi¹s with 똣at shift
direction = ³P²¹.
The question is: does 똣at shift direction = ³A² mean A -> P and ³P² P
-> A or vice versa?
A similar question was asked previously (see
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308&L=FSL&P=R26762&1
=FS
L&
9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4 ). It was suggested that
you can find out the answer to this question by running the correction
both ways (i.e. with different acquisition parameters) and see which
possibility leads to a good correction.
I have tried this by running topup and applytopup with both of the
following acquisition parameters.
0 -1 0 0.19
0 1 0 0.19
and
0 1 0 0.19
0 -1 0 0.19
Both options however lead to the exact same corrected images. Does
anyone have an explanation for this?
Kind regards, Marjolein