Or is there any way to apply TOPUP with one complete acquisition (64 read-out directions) and only one anti-parallel B0 Volume to estimate the magnetic field and use "applytopup"?
I came as far as to create the two files (which look quite good in fslview):
my_topup_results_fieldcoef.nii.gz
my_topup_results_movpar.txt.
But when I apply:
"applytopup --imain=blip_up,blip_down --inindex=1,2 --datatin=my_acq_param.txt --topup=my_topup_results --out=my_hifi_images"
the program tells me (understandably) that the two sets are mismatched and I get no results. Since I only have the 4D data set of the "blip_up" acquisition and one anti-parallel B0 volume, is there any way around that problem? If there is, how would I have to change the command line to obtain unwarped images of "blip_up" ?
Yes There is. We also had this problem and a friend explained me that there is a new version of the eddy current correction module that takes into account also my_topup_results (even if you have only one b0 in down direction) performing both eddy-current and epi-distortion correction in one step.
Thank you so much for this information. It really helps me to use our already acquired data and to avoid longer scanning times for our patients in the future
Greetings from north of the Alps
Juergen
Please contact me if you need further details. We have written a script for our pipeline that you could partially use if you need. :)
That´s just great. Thanks a lot for your offer. First, I will try to install the update and check whether it works with our data. If I encounter any problems, I would gladly contact you again.
Thank you so much
Hi, it´s me again.
I have talked to our IT specialist,who would be really grateful if we could have parts of the script for your pipeline. That would make his and my life a lot easier. If it is more convenient for you to send it to me directly, this is my email account: [email protected]
Thank you again very much
Dear Haykel Snoussi,
thank you very much for your help. Meanwhile I´ve played around a bit and I have already integrated applytopup into my script. It just works perfectly.
Thank you very much again and have a nice week-end
Jürgen
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