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.
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