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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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fc
April 17, 2015 11:23PM
Dear Daniel,

Recently I encountered a problem in MNI and Talairach coordinate conversion. I want to use some MNI coordinate from some meta-analysis, but if I input the MNI coordinate in AFNI GUI window "Jump to (MNI)", and input "0 0 0", and switch to "Where Am I?"
it shows that
//////////////////////////////////
Orignial input data coordinates in TT_N27 space

Focus point (LPI) =
-0 mm [L], -3 mm [P], 4 mm [S] {TLRC}
-0 mm [L], -0 mm [P], -0 mm {MNI} NeuroSynth SumsDB
-0 mm [L], -4 mm [P], 5 mm [S] {MNI_ANAT}

////////////////////////////////

But if I use command version whereami
$ whereami 0 0 0 -lpi
it gives
///////////////////////////////

Orignial input data coordinates in TLRC space
Focus point (LPI) =
0 mm [L], 0 mm [P], 0 mm [S] {TLRC}
0 mm [L], 0 mm [P], 0 mm [S] {MNI} <a href=...../a>
-0 mm [L], -4 mm [P], 5 mm [S] {MNI_ANAT}

/////////////////////////////

It is not the same, I see that the transform is both Brett transform.

I also use GingerALE's "Convert Foci" tool, it report Talairch coordinate in several flavours of MNI coordinate
(0,0,0) in TLRC, will be (0,0,0) in Brett MNI, (1.12, .87, -3.6) in FSL MNI, (1.04, 1.46, -4.75) in SPM MNI, and (1.08, 1.17, -4.18) in other MNI
(0,0,0) in MNI, will be (0,0,0) in Brett TLRC, (-1.07, -1.02,3.19) in FSL MNI->TLRC, (-1.02, -1.77, 4.09) in SPM MNI->TLRC, and
(-1.04, -1.39, 3.65) in other MNI->TRLC

So I am messed up by these transform, when input MNI coordinate into AFNI, some structure may display to out of brain tissue.

Thank you very much!

Best,
FC
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Subject Author Posted

MNI and TLRC coordinate question

fc April 17, 2015 11:23PM

Re: MNI and TLRC coordinate question

Daniel Glen April 19, 2015 10:18AM