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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 >