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April 27, 2022 04:37AM
Hi,

I am trying to load the brainnetome atlas as an overlay (https://afni.nimh.nih.gov/afni/community/board/read.php?1,157540,157568).

I have the atlas in AFNI_data5, so I changed to that directory and launched AFNI from there.

The output of “ls” is as follows:
@demo.Artifact           MyData                  s00.ap                     zz.errts.s620.fanaticor+orig.BRIK.gz
BN_Atlas_246_1mm.nii     index.html              s620_rest_r1+orig.BRIK.gz  zz.errts.s620.fanaticor+orig.HEAD
BN_Atlas_246_1mm.nii.gz  out.ss_review.s620.txt  s620_rest_r1+orig.HEAD

The BN_Atlas_246_1mm.nii.gz file is highlighted in red, along with the zz.errts.620.fanaticor+orig.BRIK.gz file.

When I click the overlay button in the GUI, only “s620_resr_r1” and “zz.errts.s620.fanaticor” appear – there is no sign of the BN atlas. The same applies for the underlay button. After clicking the overlay button, I see this in the terminal:

** ERROR (nifti_image_read): failed to find header file for '/home/marcus/AFNI_data5/BN_Atlas_246_1mm.nii'
** ERROR (nifti_image_read): failed to find header file for '/home/marcus/AFNI_data5/BN_Atlas_246_1mm.nii.gz'

I thought I could perhaps solve this using the “3dcopy” function, changing the file to a more AFNI-compatible file type. Here is the result of that attempt:

3dcopy BN_Atlas_246_1mm.nii.gz BN_Atlas
++ 3dcopy: AFNI version=AFNI_22.0.11 (Feb 18 2022) [64-bit]
** ERROR (nifti_image_read): failed to find header file for '/home/marcus/AFNI_data5/BN_Atlas_246_1mm.nii.gz'
** FATAL ERROR: no datasets found!
** Program compile date = Feb 18 2022

Does anyone know what the issue is here? This is my first time attempting to use AFNI so I may have missed something basic.
It could be something to do with adding the BN atlas to my ‘.afnirc’ file?

Thank you for your time,
Marcus
Subject Author Posted

Brainnetome Atlas

MarcusG April 27, 2022 04:37AM

Re: Brainnetome Atlas

ptaylor April 27, 2022 08:02AM

Re: Brainnetome Atlas

Daniel Glen April 27, 2022 11:01AM



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