I got some errors while uploading but
OAS1_0001_MR1_mpr-4_anon.img 16 MB
OAS1_0001_MR1_mpr-4_anon.hdr 348 B
Probably worked.
Thanks so much for the guide Nour! I'll try it out hoping it will work :)
I did manage to make all functions run by using
3dANALYZEtoAFNI -OK -geomparent OAS1_0236_MR2_mpr-1_anon.hdr -prefix test OAS1_0236_MR2_mpr-1_anon.hdr
3dAFNItoNIFTI -prefix nifti_file test+orig.HEAD
fslreorient2std nifti_file.nii fsl_std
robustfov -i fsl_std.nii.gz -r fsl_robust
$FSLDIR/bin/bet fsl_robust.nii.gz fsl_bet -f 0.4
But the orientation was still a bit wacky, in fsleyes the sagital slices where to the far right window (they are usually in the left window for our newer .nii files after running fslreorient2std function on them) and the BET kept the eyes (could perhaps use bet -S for that).
But something felt quite off with the orientation.
I'll try the guide and see!
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