Use the GUI to run a full registration and reformat (command -awr 01). Make sure that you specify the location of the reference brain for this project when the GUI asks you. You will have downloaded this file from http://flybrain.stanford.edu/refbrain.

The file is called:

average-goodbrains-warp40-5_e1e-2.PIC

This will generate two directories (Registration and reformatted). You can compare them with my Registration.gj directory.

If you want to see how long each registration took then look at the statistics files in each directory. You are interested in the walltime field. You can extract this information by using the unix grep tool. Here's how. Open the Terminal application (/Applications/Utilities/Terminal.app). Then type

cd /GD/projects/PN2/warpbench/Registration/

replacing the path with the appropiate location.There is a trick incidentally.If you drag the folder from the finder into the Terminal window where you are working it will paste in the full path. Then:

grep -E 'walltime( |_t)' */*.list/stat*

If you get an error, you mistyped or you are in the wrong directory.

My output looks like this (from a 4 processor G5):

affine/average-goodbrains_NCD6RLH01_9dof.list/statistics:walltime 369.000000
affine/average-goodbrains_NIA6RLH01_9dof.list/statistics:walltime 269.000000
affine/average-goodbrains_TKA7RLH01_9dof.list/statistics:walltime 225.000000
affine/average-goodbrains_TKC1RLH01_9dof.list/statistics:walltime 202.000000
affine/average-goodbrains_TKC8LLH01_9dof.list/statistics:walltime 93.000000
affine/average-goodbrains_TKC8RLH01_9dof.list/statistics:walltime 130.000000
affine/average-goodbrains_TMB2LLH01_9dof.list/statistics:walltime 327.000000
affine/average-goodbrains_TNB9R-GH14601_9dof.list/statistics:walltime 157.000000
affine/average-goodbrains_TNE7L-GH14601_9dof.list/statistics:walltime 3472.000000
affine/average-goodbrains_TSA3LLH01_9dof.list/statistics:walltime 138.000000
warp/average-goodbrains_NCD6RLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 658.000000
warp/average-goodbrains_NIA6RLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 717.000000
warp/average-goodbrains_TKA7RLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 892.000000
warp/average-goodbrains_TKC1RLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 621.000000
warp/average-goodbrains_TKC8LLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 644.000000
warp/average-goodbrains_TKC8RLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 695.000000
warp/average-goodbrains_TMB2LLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 658.000000
warp/average-goodbrains_TNB9R-GH14601_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 697.000000
warp/average-goodbrains_TNE7L-GH14601_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 750.000000
warp/average-goodbrains_TSA3LLH01_warp_m0g40c4e1e-1x16r3.list/statistics:walltime_total 631.000000

Those times are in seconds. So the whole run took a bit over 3 hours. You can see that there are very different times for different brains for the affine step. The 3000 second brain is a bit of an oddity but the time is real. It is much more reasonable on an intel mac.

Use ImageJ and the IGSRaw reader plugin. See the GUI Readme.pdf for further details. Try using the Sync Windows plugin.