NIFTI copies will be interpreted as TLRC view (not TLRC space).

AFNI Message Board
1

Hello,

I used @auto_tlrc to convert my datasets to MNI space, and then I got this warning message:


*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING:  NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING:  Consider changing the view of the dataset to TLRC view also

I’m a bit embarassed to say that I don’t understand this, but - what is the difference between space and view?
If I view my output with AFNI’s GUI - what does it mean if it is in MNI space but in ORIG view, for example?

In my particular case, the conversion was done on AFNI files (not NIFTI), so I suppose I can safely ignore this warning message, but I was still wondering regarding the difference between space and view.

Thank you (and my apologies if this is too basic, I couldn’t find an online explanation),

Galit

2

I expect these are warnings that occur during @auto_tlrc. You can safely ignore these. The warnings occur during the 3drefit commands called by that script. The warning is to let the user know that changing the space and not the view might cause problems. The “view” is essentially the AFNI format suffix, +tlrc or +orig usually. The space is the template space of the dataset - MNI, TLRC, TT_N27, D99_macaque, waxholm_rat,… @auto_tlrc applies the space of the template dataset and a +tlrc view to the output of the script, the data aligned to the template. Both NIFTI and AFNI format datasets have both a space and the equivalent of an AFNI view whenever a dataset is read into memory. You can see the space and AFNI view of all datasets in a directory with this command.

3dinfo -space -av_space -prefix *.HEAD .nii

3

Thank you, Daniel.
So just out of curiosity - what are the reprecussions of changing space (from ORIG to MNI, for example), without changing the view? If the dataset has been transformed to a template, and I read it into the GUI, what is the effect of the view format? Or is it just a technical thing of reading files?

4

For now, the afni GUI requires a similar view to see one dataset overlaying another. So both dataset would need to be either +orig or +tlrc. If you want to see a dataset that over a standard template, then you would want that dataset to be in +tlrc view.

5

Is there an override for this yet? Just a flag in .afnirc/profile or something that says "please show show me everything in “orig” space, and forget “tlrc” exists?

Thanks!

6

For datasets that have an sform or qform code = 2, AFNI_NIFTI_VIEW may be set to either orig or tlrc. Add that to your ~/.afnirc file (possibly with “@AfniEnv -set AFNI_NIFTI_VIEW orig”).

7

Thank you very much, this works well for me.