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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Kristen
October 15, 2007 08:20PM
Hi Rick,
Thanks for the advice. I don’t think I will run 3dvolreg if I am running 3dAllineate and it is already doing volume registration. However if I decide to use -1Dmatrix_* option with 3dAllienate then I will need to run 3dvolreg?

The following is the script I ran for 2dImReg/3dvolreg. (Note that 3dvolreg couldn’t run because it uses the 2dreg file that wasn’t created for the base.)

foreach run ( series1 )

2dImReg -prefix ${study}.${subject}.${run}.2dreg -dprefix ${study}.${subject}.2DREGLOG.${run} -base 3 -basefile ${study}.${subject}.${run}.aligned+orig -input ${study}.${subject}.${run}.aligned+orig

3dvolreg -clipit -dfile ${study}.${subject}.3dREGLOG.{$run} -prefix ${study}.${subject}.${run}.3dreg -base 3 ${study}.${subject}.{$run}.2dreg+orig
end

foreach run ( series2 series3 series4 )

2dImReg -prefix ${study}.${subject}.${run}.2dreg -dprefix ${study}.${subject}.2DREGLOG.${run} -base 3 -basefile ${study}.${subject}.${base_run}.aligned+orig -input ${study}.${subject}.${run}.aligned+orig

3dvolreg -clipit -dfile ${study}.${subject}.3dREGLOG.{$run} -prefix ${study}.${subject}.${run}.3dreg -base ${study}.${subject}.{$base_run}.2dreg+orig'[3]' ${study}.${subject}.${run}.2dreg+orig

end

Kristen
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Subject Author Posted

3dAllienate Error

Kristen October 13, 2007 12:35PM

Re: 3dAllienate Error

rick reynolds October 13, 2007 11:56PM

Re: 3dAllienate Error

Kristen October 14, 2007 10:32PM

Re: 3dAllienate Error

rick reynolds October 15, 2007 10:42AM

Re: 3dAllienate Error

Kristen October 15, 2007 08:20PM

Re: 3dAllienate Error

rick reynolds October 16, 2007 09:24AM

Re: 3dAllienate Error

Eric Vidoni April 08, 2008 04:08PM

Re: 3dAllienate Error

rick reynolds April 08, 2008 07:01PM

Re: 3dAllienate Error

Erika January 29, 2009 04:41PM

Re: 3dAllienate Error

Daniel Glen January 29, 2009 05:34PM

Re: 3dAllienate Error

Erika January 30, 2009 01:28PM