Thank you, Jesper. I will now test the -1/+1 and find out which one is to be used.
Nick
Niklas Lenfeldt, PhD, MSc, MAJ SWE A
Clinical Neuroscience, Umeå university
Phone: +46 70 609 66 87
Från: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
För Jesper Andersson
Skickat: den 27 februari 2016 20:42
Till: [log in to unmask]
Ämne: Re: [FSL] SV: [FSL] Acquisition parameters Philips dti data
Hi there Niklas,
you don’t actually need to get it right in this case either. The important thing in this case is to make sure that the readout time you enter for the T2 is much less than what you enter for the EPI. I would suggest for example 0.05 for
the EPI and 0.0001 for the T2.
If you can get everything right your fieldmaps will have the correct sign and be nicely scaled in Hz, but I’m guessing you don’t care about that.
Jesper
On 27 Feb 2016, at 17:22, Niklas Lenfeldt <[log in to unmask]> wrote:
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: [log in to unmask]
-----Ursprungligt meddelande-----
Från: FSL - FMRIB's Software Library [mailto:[log in to unmask]] För Andreas Bartsch
Skickat: den 11 februari 2015 10:42
Till: [log in to unmask]
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 <[log in to unmask]>:
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