UNC Infant Atlas

AFNI Message Board
1

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

2

Check that the “infant*.HEAD” datasets are in your AFNI binary directory because they are included in AFNI’s default distribution (we may stop doing that in the future to save space and download time for others). The CustomAtlases.niml filename is case sensitive, so be sure it is in that ~/UNC_Infant_Atlases directory. Use “whereami -show_atlases” to see if the niml file is being read properly.