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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joy0617
March 26, 2018 09:31PM
Hi,

I'm totally new with AFNI and working on an old dataset that has been converted to .nii format by SPM.
I thought AFNI could read .nii flies so I tried to3d directly to the structural data but it failed to output brik and head files.

to3d -spgr -session ../ -prefix RSA_S1_t1 20130912_145129t1mpragetranssrs002a1001.nii
++ to3d: AFNI version=AFNI_18.0.25 (Mar 7 2018) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
++ Counting images: total=192 2D slices
++ Each 2D slice is 448 X 512 pixels
++ Image data type = short
++ Reading images: ......................................
*+ WARNING: *** ILLEGAL INPUTS (cannot save) ***

Axes orientations are not consistent!

I tried with epi data too and got similar output. Am I doing something wrong? Should I convert these .nii files to .dcm first?

Thank you in advance!
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Subject Author Posted

using to3d with .nii data

joy0617 March 26, 2018 09:31PM

Re: using to3d with .nii data

ptaylor March 26, 2018 09:59PM

Re: using to3d with .nii data

joy0617 March 27, 2018 01:21PM

Re: using to3d with .nii data

ptaylor March 27, 2018 01:47PM

Re: using to3d with .nii data

joy0617 March 27, 2018 03:32PM

Re: using to3d with .nii data

ptaylor March 27, 2018 05:06PM