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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
