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I did indeed. So, I meant 4. Use --numprec=float Cheers MJ Begin forwarded message: > From: Mark Jenkinson <[log in to unmask]> > Date: 17 November 2008 17:15:18 GMT > To: Jesper Andersson <[log in to unmask]> > Subject: Fwd: [FSL] fnirt execution time > > Did you mean #4 to say "Use --numprec=float" ? > MJ > > > Begin forwarded message: > >> From: Jesper Andersson <[log in to unmask]> >> Date: 17 November 2008 17:09:19 GMT >> To: [log in to unmask] >> Subject: Re: [FSL] fnirt execution time >> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> >> >> 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 >> > >