Hello AFNI experts, I non-linearly warped my functional data to the MNI152_T1_2009c+tlrc.HEAD template during preprocessing. In the AFNI GUI, I changed the coordinate system to LPI-SPM and I changed the brain displays to LR mirror. Are the coordinates that I see in the AFNI GUI and the clusterize report tables that I generate in MNI space or Talairach space?
Your coordinates are in the MNI152_2009c space after the alignment process (that is, the space of your reference “base” dataset). The “+tlrc” in the file name just denotes that the dset is in some standard space (it is a legacy term from when Talairach was the only game in town, I believe).
The LR flip in the GUI just determines whether what you are seeing is: image left is subject left, or image left is subject right. (Note that you can see below is image panel telling you definitely what is what, according to your dataset info.)
The coordinate style of “LPI-SPM” is just a choice to make coords: left/posterior/inferior of the origin be negative (and those on the right/anterior/superior be positive). Note when you refer to your coordinates, you need to state that you are using the LPI coordinate system.
… but also note that you can more clearly report coords rather than, say, (-3, 47, 21) as (3L, 47A, 21S)-- that is, use the explicit part of the orientation (which is unambiguous), rather than a sign value (which can be confusing/hard to interpret), when you refer to some location.
The coordinates reported are in the space of the dataset. If you have aligned that dataset to an MNI template, then the coordinates would be in that particular template’s MNI space. Likewise, for a Talairach space template.
The coordinate order is a different question than the space they refer to. The coordinates can appear in 48 possible combinations, but in practice only two are used RAI (radiological/DICOM) and LPI (neurological/SPM). The order refers to the direction of the x,y and z coordinates. RAI is Right-to-left, Anterior-to-posterior, Inferior-to-superior. The most negative/smallest coordinates in each direction give the initials - RAI, in this case. Note that other software refer to these coordinate orders by the largest/most positive value and will use the exact opposite notation for the same coordinate order - RAI in AFNI = LPS in FreeSurfer.
The Right-left mirror in the Display control panel does not affect the coordinate order. It only affects the display of the slice. You can flip the slice with the ‘l’ (ell) key and see the lower caption will toggle between left=Left and left=Right. The coordinate order in the upper left of the AFNI GUI menu does not change with this toggle, only the slice in the image viewer. That allows the user to determine whether the left appears on the left or on the right (also anterior-posterior flipping for sagittal view). You can also set the AFNI environment variable to make whichever way you like to be permanent with AFNI_LEFT_IS_LEFT set to YES or NO in your .afnirc file in your home directory.
Thank you both for the replies!