Hi all,
I'm trying to use Freeview to display subcortical regions in aseg.mgz with a custom color lookup table. RGB colors will indicate on a jet scheme how well that region's volume correlates to performance on a behavioral measure. In other words, an R^2 coefficient of -1 is dark blue, 0 is green, and 1 is dark red. I adapted the approach for aseg structures from this method: http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/
When I try right now, by e.g. loading subjects_dir/average/mri/aseg.mgz, and choosing Color map > Lookup Table, Lookup Table > Load lookup table... and selecting my custom table file, it *almost* works. The file is copied below (it has no headers).
4 Left-Lateral-Ventricle 92 255 163 0 5 Left-Inf-Lat-Vent 224 255 31 0 7 Left-Cerebellum-White-Matter 112 255 143 0 8 Left-Cerebellum-Cortex 133 255 122 0 10 Left-Thalamus-Proper 153 255 102 0 11 Left-Caudate 102 255 153 0 12 Left-Putamen 61 255 194 0 13 Left-Pallidum 102 255 153 0 14 3rd-Ventricle 0 224 255 0 15 4th-Ventricle 61 255 194 0 16 Brain-Stem 71 255 184 0 17 Left-Hippocampus 102 255 153 0 18 Left-Amygdala 41 255 214 0 26 Left-Accumbens-area 92 255 163 0 28 Left-VentralDC 122 255 133 0 30 Left-vessel 102 255 153 0 31 Left-choroid-plexus 102 255 153 0 43 Right-Lateral-Ventricle 173 255 82 0 44 Right-Inf-Lat-Vent 122 255 133 0 41 Right-Cerebellum-White-Matter 82 255 173 0 42 Right-Cerebellum-Cortex 122 255 133 0 49 Right-Thalamus-Proper 173 255 82 0 50 Right-Caudate 143 255 112 0 51 Right-Putamen 92 255 163 0 52 Right-Pallidum 41 255 214 0 53 Right-Hippocampus 133 255 122 0 54 Right-Amygdala 20 255 235 0 58 Right-Accumbens-area 82 255 173 0 60 Right-VentralDC 122 255 133 0 62 Right-vessel 122 255 133 0 63 Right-choroid-plexus 143 255 112 0 72 5th-Ventricle 92 255 163 0 85 Optic-Chiasm 112 255 143 0 251 CC_Posterior 71 255 184 0 252 CC_Mid_Posterior 31 255 224 0 253 CC_Central 10 255 245 0
The index numbers were chosen to match those found in the default aseg LUT, as listed on the FS wiki: FSTutorial > AnatomicalROI > FreeSurferColorLUT. Some regions appear correctly, but others either a) display with incorrect labels, particularly Right-Cerebellum-White-Matter or Right-Cerebellum-Cortex on *cortical* white matter and ribbon, or b) display with no label in the info panel, which makes it unclear whether it's working.
Notes: - Originally indices were simply 1 to n, but that caused a wider array of problems, and I inferred (perhaps incorrectly) freeview was matching regions with indices rather than label names. -This particular map is mostly green since most correlations are small, which is fine; others will have a broader range of values. -I'm not sure what the effect is of pressing the "Show existing labels only" toggle, which eliminates a couple areas from the label list, but it's unclear how it chooses them.
Can anyone offer advice on how to ensure the correct colors are displayed in the correct regions? (Or an easier way to do this?)
Cheers, C.P. Frost UW-Madison
Try loading aseg.mgz as the aux volume so you can see the number at a particular voxel. If the color is not correct, see what the number is and what it corresponds to in the LUT doug
On 08/19/2014 05:57 PM, C.P. Frost wrote:
Hi all,
I'm trying to use Freeview to display subcortical regions in aseg.mgz with a custom color lookup table. RGB colors will indicate on a jet scheme how well that region's volume correlates to performance on a behavioral measure. In other words, an R^2 coefficient of -1 is dark blue, 0 is green, and 1 is dark red. I adapted the approach for aseg structures from this method: http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/
When I try right now, by e.g. loading subjects_dir/average/mri/aseg.mgz, and choosing Color map > Lookup Table, Lookup Table > Load lookup table... and selecting my custom table file, it *almost* works. The file is copied below (it has no headers).
4 Left-Lateral-Ventricle 92 255 163 0 5 Left-Inf-Lat-Vent 224 255 31 0 7 Left-Cerebellum-White-Matter 112 255 143 0 8 Left-Cerebellum-Cortex 133 255 122 0 10 Left-Thalamus-Proper 153 255 102 0 11 Left-Caudate 102 255 153 0 12 Left-Putamen 61 255 194 0 13 Left-Pallidum 102 255 153 0 14 3rd-Ventricle 0 224 255 0 15 4th-Ventricle 61 255 194 0 16 Brain-Stem 71 255 184 0 17 Left-Hippocampus 102 255 153 0 18 Left-Amygdala 41 255 214 0 26 Left-Accumbens-area 92 255 163 0 28 Left-VentralDC 122 255 133 0 30 Left-vessel 102 255 153 0 31 Left-choroid-plexus 102 255 153 0 43 Right-Lateral-Ventricle 173 255 82 0 44 Right-Inf-Lat-Vent 122 255 133 0 41 Right-Cerebellum-White-Matter 82 255 173 0 42 Right-Cerebellum-Cortex 122 255 133 0 49 Right-Thalamus-Proper 173 255 82 0 50 Right-Caudate 143 255 112 0 51 Right-Putamen 92 255 163 0 52 Right-Pallidum 41 255 214 0 53 Right-Hippocampus 133 255 122 0 54 Right-Amygdala 20 255 235 0 58 Right-Accumbens-area 82 255 173 0 60 Right-VentralDC 122 255 133 0 62 Right-vessel 122 255 133 0 63 Right-choroid-plexus 143 255 112 0 72 5th-Ventricle 92 255 163 0 85 Optic-Chiasm 112 255 143 0 251 CC_Posterior 71 255 184 0 252 CC_Mid_Posterior 31 255 224 0 253 CC_Central 10 255 245 0
The index numbers were chosen to match those found in the default aseg LUT, as listed on the FS wiki: FSTutorial > AnatomicalROI > FreeSurferColorLUT. Some regions appear correctly, but others either a) display with incorrect labels, particularly Right-Cerebellum-White-Matter or Right-Cerebellum-Cortex on *cortical* white matter and ribbon, or b) display with no label in the info panel, which makes it unclear whether it's working.
Notes:
- Originally indices were simply 1 to n, but that caused a wider array
of problems, and I inferred (perhaps incorrectly) freeview was matching regions with indices rather than label names. -This particular map is mostly green since most correlations are small, which is fine; others will have a broader range of values. -I'm not sure what the effect is of pressing the "Show existing labels only" toggle, which eliminates a couple areas from the label list, but it's unclear how it chooses them.
Can anyone offer advice on how to ensure the correct colors are displayed in the correct regions? (Or an easier way to do this?)
Cheers, C.P. Frost UW-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
C.P. Frost -
Douglas N Greve