On Wed, 5 Sep 2018 15:16:50 -0400, Ricardo Valle <[log in to unmask]> wrote:
Hi Ruy,
Thanks for the reply! I am using a remote computer cluster (my computer is a PC) so my allocated memory is a bit low (about 2000 MB). I am confused though, as in the past I have run this command on a different data set (similar size) without a problem. I have sporadic access to a Mac w/ FSL and much more RAM, I can try on there to see if that will work.
Thanks!
Josh
>Hi Josh,
>
>My initial guess is you don’t have enough RAM. “Killed” usually happens when your system is out of memory. How much RAM do you have? What OS are you on?
>
>Best,
>Ruy
>> On Sep 5, 2018, at 3:12 PM, Josh Robinson <[log in to unmask]> wrote:
>>
>> Hello FSL experts,
>>
>> I am running into a problem trying to run eddy on my data. I'm trying to run data acquired with a Philips scanner, (single shot, echo spacing=.69902, epi factor=41, per MR tech). Our data has 32 DW volumes, plus one b0 acquired at the end, A>P. Unfortunately only the single b0 and no other scans running in the other direction that could be run through topup. My command is:
>>
>> eddy_openmp --imain=data.nii --mask=b0_ss_mask.nii --index=index.txt --acqp=acqp.txt --bvecs=data.bvec --bvals=data.bval --out
>>
>> It runs for a few minutes until it tries to calculate parameter updates, then prints "Killed" and terminates. Bvals and bvecs reflect the number of volumes in data, acqp (dwelltime=0.027) and index should accurately reflect the acquisition parameters.
>>
>> Your help is greatly appreciated.
>>
>> JoshRobinson
>>
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