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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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nibhroim
June 06, 2018 06:07AM
Hi there,

I'm hoping you can help me.

In order to use the UNC Infant atlas
I renamed the CustomAtlases.niml and put in directory ~/UNC_Infant_Atlases

I then - Set AFNI to use this supplemental atlas directory with this (removing the #) :
@AfniEnv -set AFNI_SUPP_ATLAS_DIR ~/UNC_Infant_Atlases
@AfniEnv -set AFNI_ATLAS_COLORS infant-1yr-aal
@AfniEnv -set AFNI_TEMPLATE_SPACE_LIST unc_infant_neo,unc_infant_1yr,unc_infant_2yr
@AfniEnv -set AFNI_ATLAS_LIST ALL

When I typed in whereami -show_atlas_code it said there was no header file for infant aal 1yr, neo aal or 2yr aal.
I did 3dcopy infant-1yr-aal.nii.gz to infant 1-yr-aal and the same for neo and 2yr to create these header files.
After this when I typed in whereami -show_atlas_code no error came up.

However, then when I loaded afni and went define datamode - plugins and tried to select for regions within the atlas I receive this error again.

** ERROR (nifti_image_read): failed to find header file for 'infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/fsfast/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/tktools/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/fsl/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/mni/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/fsl/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/fsfast/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/tktools/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/fsl/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/freesurfer/mni/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/fsl/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/games/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/games/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/snap/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/workbench/bin_linux64/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for 'bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for 'usr/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/sbin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/games/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/games/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for 'snap/bin/infant-1yr-aal.nii.gz'
** ERROR (nifti_image_read): failed to find header file for '/usr/local/workbench/bin_linux64/infant-1yr-aal.nii.gz'

Do you have any advice for how to fix this?

Best wishes,
Megan
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Subject Author Posted

UNC Infant Atlas

nibhroim June 06, 2018 06:07AM

Re: UNC Infant Atlas

Daniel Glen June 06, 2018 01:54PM