====== Gordon + Harvard-Oxford Atlas ======
An atlas that combines [[:tools:gordonatlas|Gordon Atlas]] and [[:tools:haroxatlas]]
''rhea:/opt/ni_tools/atlas/GordonHarOx/Gordon_HarOx_1mm+tlrc.HEAD ''
The first 333 are [[:tools:gordonatlas|Gordon Atlas]], the next 12 are from harox (numbered 333+1:12 -- not matching original harox value)
^roi^orig values L,R^ in combined ^
|thalamus | 4,15 | 334,340 |
|amygdala | 10,20| 338,344 |
|nacc | 11,21| 339,345 |
|putamen | 6,17 | 336,342 |
|caudate | 5,16 | 335,341 |
|pallidum | 7,18 | 337,343 |
===== Info =====
==== 3dNotes ====
Created like
3dNotes /opt/ni_tools/atlas/GordonHarOx/Gordon_HarOx_1mm+tlrc.HEAD
----- HISTORY -----
....
[lncd@skynet.local: Mon Oct 17 17:08:01 2016] 3dcalc -a HarOx-sub-1mm+tlrc.
-expr '1*equals(a,4) + 2*equals(a,5) + 3*equals(a,6) + 4*equals(a,7) + 5*equals(a,10) +
6*equals(a,11) + 7*equals(a,15) + 8*equals(a,16) + 9*equals(a,17) +
10*equals(a,18) + 11*equals(a,20) + 12*equals(a,21)'
-prefix HarOx-sub-1mm-mod+tlrc
....
[lncd@skynet.local: Mon Oct 17 17:09:28 2016] 3dcalc -a Parcels_MNI_111_warped.nii.gz -b HarOx-sub-1mm-mod+tlrc.
-expr 'a + (333*ispositive(b-0.5) + b)*equals(a,0)'
-prefix Gordon_HarOx_1mm+tlrc
==== whereami ====
whereami \
-omask '/opt/ni_tools/atlas/GordonHarOx/Gordon_HarOx_1mm+tlrc.HEAD<334..336>' \
-atlas FS.afni.MNI2009c_asym
++ Input coordinates orientation set by default rules to RAI
++ In ordered mode ...
++ Have 4 unique values of:
0 334 335 336
++ Skipping unique value of 0
++ ========================================================================
++ Processing unique value of 334
++ 10907 voxels in ROI
++ 10907 voxels in atlas-resampled mask
Intersection of ROI (valued 334) with atlas FS.afni.MNI2009c_asym (sb0):
81.6 % overlap with Left-Thalamus-Proper, code 7
3.8 % overlap with Left-VentralDC, code 18
0.6 % overlap with Left-Caudate, code 8
0.5 % overlap with Brain-Stem, code 13
0.3 % overlap with Left-Hippocampus, code 14
-----
86.8 % of cluster accounted for.
++ ========================================================================
++ Processing unique value of 335
++ 4444 voxels in ROI
++ 4444 voxels in atlas-resampled mask
Intersection of ROI (valued 335) with atlas FS.afni.MNI2009c_asym (sb0):
82.6 % overlap with Left-Caudate, code 8
0.1 % overlap with Left-Thalamus-Proper, code 7
0.0 % overlap with Left-Putamen, code 9
-----
82.7 % of cluster accounted for.
++ ========================================================================
++ Processing unique value of 336
++ 6612 voxels in ROI
++ 6612 voxels in atlas-resampled mask
Intersection of ROI (valued 336) with atlas FS.afni.MNI2009c_asym (sb0):
81.3 % overlap with Left-Putamen, code 9
2.5 % overlap with Left-Pallidum, code 10
0.0 % overlap with ctx-lh-insula, code 80
-----
83.7 % of cluster accounted for.