Hi Neda,
It does look like you are running out of RAM. Are you running any
other software at the same time?
What are the dimensions of your EPI and T1 images? You can find out
with fslinfo. If you have acquired a lot of diffusion directions,
and/or your T1 image is high resolution (e.g. 0.5mm isotropic), then
you might still be running into RAM issues.
One option you have is to use a single 3D image from your diffusion
data as input to epi_reg, instead of the full 4D data set.
And the step which is failing is actually the final step in epi_reg,
where the input EPI data is transformed into structural space. If you
are only interested in the registration files (i.e. the .mat and _warp
files), then you can safely ignore the error.
Cheers,
Paul
On 09/06/2019, Neda Mohammadi <[log in to unmask]> wrote:
> Hi Paul,
>
> Thanks for your replay.
>
> No, i don't use from VM.
> i'm working with this system:
> Intel® Core™ i7-6700 CPU @ 3.40GHz × 8
> UBUNTU 16.0.4 LTS
> RAm: 8 G
>
>
> On Sun, Jun 2, 2019, 18:11 paul mccarthy <[log in to unmask]> wrote:
>
>> Hi Neda,
>>
>> It looks like you might have run out of RAM, and your operating system
>> killed the process.
>>
>> Are you running in a VM? If so, try increasing the available RAM.
>>
>> Cheers,
>>
>> Paul
>>
>> On 02/06/2019, Neda Mohammadi <[log in to unmask]> wrote:
>> > Dear FSL experts,
>> >
>> > I'm trying to register epi (DTI image) to structural (T1) with
>> > "epi-reg"
>> > command-line ( in FSL version 5.0.11), but when I run this command, It
>> > returns this error:
>> >
>> > Running FAST segmentation
>> > FLIRT pre-alignment
>> > Registering fieldmap to structural
>> > Running BBR with fieldmap
>> > 0.515228 0.999827 0.008908 -0.016327 0.000000 -0.009692 0.998773
>> -0.048561
>> > 0.000000 0.015874 0.048711 0.998687 0.000000 -0.653856 -7.938320
>> 12.613359
>> > 1.000000
>> > Making warp fields and applying registration to EPI series
>> > /usr/local/fsl/bin/epi_reg: line 392: 4369 Killed
>> > $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} -w
>> ${vout}_warp
>> > --interp=spline --rel
>> >
>> > Any help would be greatly appreciated.
>> > --
>> > *Best Regards,*
>> > *Neda*
>> >
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