Dear Jesper
Thanks for answering. My reference image is of size 80 x 35 x 12 x 360 with
0.2 x 0.2 x 0.5 mm.
What would you propose as warp resolution and intensity model?
Cheers
Rafael
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag
von Jesper Andersson
Gesendet: Freitag, 5. Juni 2015 10:47
An: [log in to unmask]
Betreff: Re: [FSL] FNIRT error (out of memory)
Dear Rafael,
what size is your reference image? That will be important in deciding the
memory requirements.
In your fnirt call below you haven’t specified your warp resolution. Nor
have you specified an intensity model. The easiest way to run fnirt is to
use a configuration file that specifies all the options. If the ones we
supply don’t fit your purpose it is often a good idea to still start with
one of them as a basis for editing.
Jesper
On 3 Jun 2015, at 23:33, Rafael Wampfler <[log in to unmask]> wrote:
> Dear all
>
> I have a set of fMRI images with dimension 80 x 35 x 12 x 360 and 0.2 x
0.2 x 0.5 mm. I'm choosing one of the images a my reference image, then I
want to register the other images to this reference image. First, I divide
both the reference image and the other images into 3D volumes. My problem is
now that I'm getting an error in fnirt when I'm trying to register such a 3D
volume to the 3D volume of my reference image (Before running fnirt I have
run flirt).
>
> When I apply fnirt I'm getting almost immediately the following error:
>
> Error occurred when preparing to fnirt Exception thrown with message:
> std::bad_alloc
>
> I have it run on my machine as well as on a cluster. After some
investigations I think that the problem is due to "out of memory" but I
don't know why and how I can fix it.
>
> My command is the following:
>
> fnirt --in=3D Volume \
> --ref=3D Volume Of Reference Image \
> --refmask=Mask Of Reference Image (which I have created
for brain extraction) \
> --iout=Output File Name \
> --aff=Transformation matrix created by flirt \
> --miter=5,5,5,5,5,10 \
> --infwhm=8,6,5,4.5,3,2 \
> --reffwhm=8,6,5,4,2,0 \
> --estint=1,1,1,1,1,0 \
> --applyrefmask=1,1,1,1,1,1 \
> --applyinmask=1 \
> --subsamp=4,4,2,2,1,1 \
> --lambda=400,200,150,75,60,45 \
> --cout=Cout file name
>
>
>
> Does somebody have a guess what the problem could be? I can also provide
the full script when it is of help.
>
> Thank you very much.
|