Thank you for responding.

I now understand that the output from plugout_drive is sent to afni instead of the stdout but I am not really sure what your code is trying to do. When I run it, I get this output:

x1b[1;31mx1b[0m
x1b[1;31mThanks go to T Holroyd for useful feedbackx1b[0m
x1b[1;31mx1b[0m
x1b[1;31mInitializing: X11.. Widgets.. Input files:x1b[0m
x1b[1;31m session #  1  = /afni/ ==> 11 datasetsx1b[0m
x1b[1;31m dataset count = 11x1b[0m
x1b[31m....x1b[0m
x1b[31m  NLfit & NLerr= Optimizer (AFNI_NLFIM_METHOD) is SIMPLEXx1b[0m
x1b[1;31m Time series   = 5 files readx1b[0m
x1b[1;31m Plugins       = 52 libraries readx1b[0m
x1b[1;31m Plugouts      = listening for connectionsx1b[0m
x1b[1;31mreading CTSDE_REGtoanatr1_resampled+orig(432 million [mega] bytes)..donex1b[0m
x1b[1;31mx1b[0m
x1b[1;31m++ NOTE: This version of AFNI was built Mar  9 2015 ++x1b[0m
x1b[1;31m++ NOTE: 'Define Markers' is hidden: right-click 'DataDir' to see itx1b[0m
x1b[1;31m++ AFNI is detached from terminal.x1b[0m
x1b[1m++ AFNI control channel tcp:localhost:7955 createdx1b[0m
x1b[1m++ AFNI control channel connectedx1b[0m
x1b[1m++ Sending control information to AFNIx1b[0m
x1b[1m   PONAME ManOfLaManchax1b[0m
x1b[1mIOCHAN tcp:localhost:8099x1b[0m
x1b[1;31mPO: plugout connection from host 127.0.0.1 (tcp:*:7955)x1b[0m
x1b[1m++ AFNI data channel createdx1b[0m
Enter command: x1b[1m++ AFNI data channel is openx1b[0m
x1b[1;31mPO: plugout connection name is ManOfLaManchax1b[0m

GET_DICOM_XYZ

++ AFNI response string: OK!

Enter command: QUIT

x1b[1;31mx1b[0m
x1b[1;31m******* AFNI is commanded to quit! *******x1b[0m
x1b[1;31mx1b[0m
x1b[1;31mx1b[0m
x1b[1;31m** AFNI terminates: If you have tears, prepare to shed them now!x1b[0m
x1b[1;31mx1b[0m
x1b[31m  NLfit & NLerr= Found 28 modelsRAI xyz: 0.198189 -44.508759 27.268639x1b[0m
x1b[1m** AFNI data channel aborted!x1b[0m

You can see on the second to last line that the coordinates are printed out but that is only after I quit afni. I am also not sure what your sed commands are trying to do or how I am suppose to use this redirection to save the coordinates. I don't have a lot of experience with bash so if you could explain how the code is suppose to function, I would greatly appreciate it.

Thank you for your help
Matthew



Edited 1 time(s). Last edit at 06/02/2015 04:51PM by rollom.