History of AFNI updates  

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April 27, 2022 08:02AM
Hi, Marcus-

Datasets have "view" and "space" properties---see slides 33-36 here:
afni_open -aw afni30_vol_dset_basics.pdf

These record/mark when a dataset is in a standard space of some kind (MNI, IBT, TLRC, NMT, etc.) vs in "original"/subject space. If you see the BRIK/HEAD file have "+orig" in it, it is in 'orig' space. If it has '+tlrc', it is in some kind of standard space (confusingly, not necessarily Talairach-Tournoux specifically). You can also use:
3dinfo -av_space -space -prefix DSET1 DSET2 ...
to see the "view space" and specific space names on any dset (NIFTI, BRIK/HEAD, etc.)

The GUI does not allow "orig" and "tlrc" dsets to be overlaid. By looking at the name, I can see that "zz.errts.s620.fanaticor+orig.HEAD" is in orig space, and I am guessing that BN_Atlas_246_1mm.nii is in standard space. You can verify this mismatch of views with:
3dinfo -av_space -space -prefix zz.errts.s620.fanaticor+orig.HEAD BN_Atlas_246_1mm.nii
Is that *errts* file from afni_proc.py? Was a "tlrc" block used there, and are you sure that dataset should be overlayable on a template (i.e., did it get aligned to that space during processing)?

If you want to view that dset on a standard space template, you can use 3drefit to alter its header properties. Because 3drefit does *not* create a new dset, you should copy it first:
3dcopy zz.errts.s620.fanaticor+orig.HEAD  NEW_zz.errts.s620.fanaticor
3drefit -space TLRC -view tlrc NEW_zz.errts.s620.fanaticor+orig
... after which, you will see the NEW* file listed as "NEW_zz.errts.s620.fanaticor+tlrc.*", and that should be overlayable on the other standard space data. (NB: any dataset with a standard space should be overlayable, they don't need to all be specifically MNI or TLRC, say. If the brainnetome space is MNI specifically, you could put "3drefit -space MNI -view tlrc NEW_zz.errts.s620.fanaticor+orig", if you wanted.)

--pt
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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