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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CeliaG
July 29, 2015 09:17AM
P.S. These are the scripts I tried. (Could you please tell me what a base is, and how I get one? transformation matrix to rotate my pig brain MRI maybe? I have no idea how to get this)



- Celia


[imac-de-claire-mazzocco:Celia/150304minipig450254/T1] celiagellman% 3dQwarp -source r01_MC+orig.HEAD -prefix qwarp-output-r01_MC+orig -lpc -verb -iwarp -blur 0 3
++ OpenMP thread count = 2
++ 3dQwarp: AFNI version=AFNI_2011_12_21_1014 (Jul 17 2015) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./r01_MC+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./r01_MC+orig.BRIK is 21.963942 degrees from plumb.
** ERROR: You can't use -source without -base!
** FATAL ERROR: Cannot continue after above error
** Program compile date = Jul 17 2015
[imac-de-claire-mazzocco:Celia/150304minipig450254/T1] celiagellman% 3dWarp -deoblique -source r01_MC+orig.HEAD -prefix qwarp-output-r01_MC+orig
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (Jul 17 2015) [64-bit]
++ Authored by: RW Cox
** ERROR: Unknown option -source
Here's hoping these excerpts from '3dWarp -help' enlighten:
'-cubic } = Chooses spatial interpolation method.'
'-oblique_parent obl_dset = Read in the oblique transformation matrix'
'-deoblique or'
[imac-de-claire-mazzocco:Celia/150304minipig450254/T1] celiagellman%




[imac-de-claire-mazzocco:Celia/150304minipig450254/T1] celiagellman% 3dQwarp -source r01_MC+orig.HEAD -prefix qwarp-output-r01_MC+orig -lpc -verb -iwarp -blur 0 3
++ OpenMP thread count = 2
++ 3dQwarp: AFNI version=AFNI_2011_12_21_1014 (Jul 17 2015) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./r01_MC+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./r01_MC+orig.BRIK is 21.963942 degrees from plumb.
** ERROR: You can't use -source without -base!
** FATAL ERROR: Cannot continue after above error
** Program compile date = Jul 17 2015
[imac-de-claire-mazzocco:Celia/150304minipig450254/T1] celiagellman% 3dWarp -deoblique -source r01_MC+orig.HEAD -prefix qwarp-output-r01_MC+orig
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (Jul 17 2015) [64-bit]
++ Authored by: RW Cox
** ERROR: Unknown option -source
Here's hoping these excerpts from '3dWarp -help' enlighten:
'-cubic } = Chooses spatial interpolation method.'
'-oblique_parent obl_dset = Read in the oblique transformation matrix'
'-deoblique or'
[imac-de-claire-mazzocco:Celia/150304minipig450254/T1] celiagellman%
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Subject Author Posted

using 3dWarp?

CeliaG July 29, 2015 08:36AM

Re: using 3dWarp?

CeliaG July 29, 2015 09:17AM

Re: using 3dWarp?

rick reynolds July 29, 2015 09:50AM

Re: using 3dWarp?

CeliaG July 30, 2015 08:00AM