AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Whitney
October 28, 2005 04:45PM
Assisted by Peggy's superb hands-on handout from Bootcamp 2005, I have successfully vol-reg'd the 8 EPI's from a pilot fMRI session to the 105th volume of the 8th EPI. Nevertheless, I had to do so by volreg-ing each EPI in turn, for my efforts to use a loop at the command line kept meeting with the following error message: "run: Undefined variable."

Here is the exact command that I tried to implement:
foreach run (1 2 3 4 5 6 7 8) 3dvolreg -base JIepi8+orig'[105]' -tshif t 0 -prefix JIepi{$run}_vr JIepi{$run}+orig'[2..134]' end

The EPI files listed in the directory in which I was working have the following names:
JIepi1+orig.BRIK JIepi3+orig.BRIK JIepi5+orig.BRIK JIepi7+orig.BRIK
JIepi1+orig.HEAD JIepi3+orig.HEAD JIepi5+orig.HEAD JIepi7+orig.HEAD
JIepi2+orig.BRIK JIepi4+orig.BRIK JIepi6+orig.BRIK JIepi8+orig.BRIK
JIepi2+orig.HEAD JIepi4+orig.HEAD JIepi6+orig.HEAD JIepi8+orig.HEAD

Ideas, anyone? Thanks! -Whitney

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Subject Author Posted

foreach loop error

Whitney October 28, 2005 04:45PM

Re: foreach loop error

rick reynolds October 28, 2005 05:01PM

Re: foreach loop error

Whitney October 31, 2005 11:12AM