Date: 17 November 2008 17:09:19 GMT
Subject: Re: [FSL] fnirt execution time
Dear Xiujuan,
I was using fnirt and it took many hours (>6) to register two images. Is it a
normal run time or did I do something wrong? The input images have a voxel
dimension of 128x160x128, and I used the default parameter settings. The
images were affine-aligned already, so I didn't do it again. The log file is
attached. How can I improve the efficiency besides cropping the input images
to a smaller size and specifying a subsampling of 2 at the lowest level? Thanks!
It seems you have run it with the "default default" parameters. I would instead recommend you to start with one of the configuration files (e.g. the T1->MNI152 one) and then make changes to that for your specific case.
As for execution time it does sound much. One thing to look out for is if it starts to page/swap or not. If your machine is able to hold everything in RAM, rather than having to swap things back and forth to disc, things will be much smoother. The things I would suggest to do is
1. Specify subsampling 2 at lowest level. You do not really need a resolution higher than 2mm in the images to estimate warps with 10mm. The 2-3mm image resolution you get from a subsampling of 2 is more than sufficient. You should also be aware that this does NOT mean that your results will have a 2mm resolution. They will have the original resolution and will be in the space of the image you specifies as --ref.
2. Crop the image you use as --ref. Make sure that the image-matrix is "tight" around the brain in the image you use as --ref. Have a look at the MNI152 images to get an idea of what I mean by "tight".
3. Use --splineorder=2.
This will have an impact both on the amount of calculations that are performed, and on the RAM needed. If you
4. Use --numprec=double.
This will have an impact on the RAM needed.
Good luck Jesper