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,