Beauchamp:AutomatingAFNI: Difference between revisions
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(New page: Many times it is useful to automate AFNI and SUMA. For instance, if you have scanned 20 subjects and would like to print out the results of your analysis for each one without having to man...) |
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For AFNI, the program to use is plugout_drive. Here are some sample commands to load AFNI and set the viewer settings. It is good to wait for AFNI to load before sending commands, hence to "sleep" command. | For AFNI, the program to use is plugout_drive. Here are some sample commands to load AFNI and set the viewer settings. It is good to wait for AFNI to load before sending commands, hence to "sleep" command. | ||
echo "wait 10 seconds" \ | echo "wait 10 seconds" \ | ||
sleep 10 \ | sleep 10 \ | ||
plugout_drive -com 'SWITCH_UNDERLAY anatavg' \ | plugout_drive -com 'SWITCH_UNDERLAY anatavg' \ | ||
-com 'SWITCH_OVERLAY stats.{$s}_MoEy' \ | -com 'SWITCH_OVERLAY stats.{$s}_MoEy' \ | ||
-quit | -quit | ||
plugout_drive -com 'SET_FUNCTION stats.PL_MoEy[0 11 0]' -quit | |||
plugout_drive -com 'SET_THRESHOLD A.5000 1' -quit | |||
plugout_drive -com 'SET_FUNCTION stats.PL_MoEy[0 11 0]' -quit | plugout_drive -com 'SET_PBAR_ALL A.-7 40.0=yellow 26.4=oran-yell 13.2=oran-red 2.0=green -2.0=blue -13.2=lt-blue1 -26.4=lt-blue2 -40=blue-cyan' -quit | ||
plugout_drive -com 'SET_THRESHOLD A.5000 1' -quit | plugout_drive -com 'SET_FUNC_RANGE 1' -quit | ||
plugout_drive -com 'SET_PBAR_ALL A.-7 40.0=yellow 26.4=oran-yell 13.2=oran-red 2.0=green -2.0=blue -13.2=lt-blue1 -26.4=lt-blue2 -40=blue-cyan' -quit | |||
plugout_drive -com 'SET_FUNC_RANGE 1' -quit | |||
Revision as of 13:44, 14 February 2017
Many times it is useful to automate AFNI and SUMA. For instance, if you have scanned 20 subjects and would like to print out the results of your analysis for each one without having to manually set the viewer settings for each subjects. For AFNI, the program to use is plugout_drive. Here are some sample commands to load AFNI and set the viewer settings. It is good to wait for AFNI to load before sending commands, hence to "sleep" command.
echo "wait 10 seconds" \
sleep 10 \
plugout_drive -com 'SWITCH_UNDERLAY anatavg' \
-com 'SWITCH_OVERLAY stats.{$s}_MoEy' \
-quit
plugout_drive -com 'SET_FUNCTION stats.PL_MoEy[0 11 0]' -quit
plugout_drive -com 'SET_THRESHOLD A.5000 1' -quit
plugout_drive -com 'SET_PBAR_ALL A.-7 40.0=yellow 26.4=oran-yell 13.2=oran-red 2.0=green -2.0=blue -13.2=lt-blue1 -26.4=lt-blue2 -40=blue-cyan' -quit
plugout_drive -com 'SET_FUNC_RANGE 1' -quit
