Automatically loading colormaps for customized segmentations

[zhengchencai]

Hello,

I have a segmentation NIfTI file (aparc+aseg+vep.nii) and a LUT file (VEP_atlas_AFNI.lt) that mimics the AFNI .lt format as follows,

<VALUE_LABEL_DTABLE
ni_type="2*String"
ni_dimen="200"
pbar_name="VEP_atlas">
"0" "Unknown"
"1" "Left-Cerebral-Exterior"
"2" "Left-Cerebral-White-Matter"
"3" "Left-Cerebral-Cortex"
"4" "Left-Lateral-Ventricle"
"5" "Left-Inf-Lat-Vent"
"6" "Left-Cerebellum-Exterior"
"7" "Left-Cerebellum-White-Matter"
"8" "Left-Cerebellum-Cortex"
"9" "Left-Thalamus"
"10" "Left-Thalamus-Proper"
"11" "Left-Caudate"
"12" "Left-Putamen"
"13" "Left-Pallidum"
"14" "3rd-Ventricle"
"15" "4th-Ventricle"
"16" "Brain-Stem"
"17" "Left-Hippocampus"
"18" "Left-Amygdala"
"19" "Left-Insula"
"20" "Left-Operculum"
"21" "Line-1"
"22" "Line-2"
"23" "Line-3"
"24" "CSF"
"25" "Left-Lesion"
"26" "Left-Accumbens-area"
"27" "Left-Substancia-Nigra"
"28" "Left-VentralDC"
"29" "Left-undetermined"
"30" "Left-vessel"
"31" "Left-choroid-plexus"
"32" "Left-F3orb"
"33" "Left-lOg"
"34" "Left-aOg"
"35" "Left-mOg"
"36" "Left-pOg"
"37" "Left-Stellate"
"38" "Left-Porg"
"39" "Left-Aorg"
"40" "Right-Cerebral-Exterior"
"41" "Right-Cerebral-White-Matter"
"42" "Right-Cerebral-Cortex"
"43" "Right-Lateral-Ventricle"
"44" "Right-Inf-Lat-Vent"
"45" "Right-Cerebellum-Exterior"
"46" "Right-Cerebellum-White-Matter"
"47" "Right-Cerebellum-Cortex"
"48" "Right-Thalamus"
"49" "Right-Thalamus-Proper"
"50" "Right-Caudate"
"51" "Right-Putamen"
"52" "Right-Pallidum"
"53" "Right-Hippocampus"
"54" "Right-Amygdala"
"55" "Right-Insula"
"56" "Right-Operculum"
"57" "Right-Lesion"
"58" "Right-Accumbens-area"
"59" "Right-Substancia-Nigra"
"60" "Right-VentralDC"
"61" "Right-undetermined"
"62" "Right-vessel"
"63" "Right-choroid-plexus"
"64" "Right-F3orb"
"65" "Right-lOg"
"66" "Right-aOg"
"67" "Right-mOg"
"68" "Right-pOg"
"69" "Right-Stellate"
"70" "Right-Porg"
"71" "Right-Aorg"
"72" "5th-Ventricle"
"73" "Left-Interior"
"74" "Right-Interior"
"77" "WM-hypointensities"
"78" "Left-WM-hypointensities"
"79" "Right-WM-hypointensities"
"80" "non-WM-hypointensities"
"81" "Left-non-WM-hypointensities"
"82" "Right-non-WM-hypointensities"
"83" "Left-F1"
"84" "Right-F1"
"85" "Optic-Chiasm"
"192" "Corpus_Callosum"
"251" "CC_Posterior"
"252" "CC_Mid_Posterior"
"253" "CC_Central"
"254" "CC_Mid_Anterior"
"255" "CC_Anterior"
"1000" "ctx-lh-unknown"
"2000" "ctx-rh-unknown"
"71001" "Left-Frontal-pole"
"71002" "Left-Orbito-frontal-cortex"
"71003" "Left-Gyrus-rectus"
"71004" "Left-F3-Pars-Orbitalis"
"71005" "Left-F3-Pars-triangularis"
"71006" "Left-F3-pars-opercularis"
"71007" "Left-Inferior-frontal-sulcus"
"71008" "Left-F2-rostral"
"71009" "Left-F2-caudal"
"71010" "Left-Middle-frontal-sulcus"
"71011" "Left-SFS-rostral"
"71012" "Left-SFS-caudal"
"71013" "Left-F1-mesial-prefrontal"
"71014" "Left-PreSMA"
"71015" "Left-SMA"
"71016" "Left-F1-lateral-prefrontal"
"71017" "Left-F1-lateral-premotor"
"71018" "Left-Subcallosal-area"
"71019" "Left-Precentral-sulcus-inferior-part"
"71020" "Left-Precentral-sulcus-superior-part"
"71021" "Left-Precentral-gyrus-head-face"
"71022" "Left-Precentral-gyrus-upper-limb"
"71023" "Left-Central-sulcus-head-face"
"71024" "Left-Central-sulcus-upper-limb"
"71025" "Left-Paracentral-lobule"
"71026" "Left-Central-operculum"
"71027" "Left-Parietal-operculum"
"71028" "Left-Anterior-cingulate-cortex"
"71029" "Left-Middle-cingulate-cortex-anterior-part"
"71030" "Left-Middle-cingulate-cortex-posterior-part"
"71031" "Left-Posterior-cingulate-cortex-dorsal"
"71032" "Left-Posterior-cingulate-cortex-retrosplenial-gyrus"
"71033" "Left-Insula-gyri-brevi"
"71034" "Left-Insula-gyri-longi"
"71035" "Left-Temporal-pole"
"71036" "Left-T1-planum-polare"
"71037" "Left-Gyrus-of-Heschl"
"71038" "Left-T1-planum-temporale"
"71039" "Left-T1-lateral-anterior"
"71040" "Left-T1-lateral-posterior"
"71041" "Left-STS-anterior"
"71042" "Left-STS-posterior"
"71043" "Left-ITS-anterior"
"71044" "Left-ITS-posterior"
"71045" "Left-T2-anterior"
"71046" "Left-T2-posterior"
"71047" "Left-T3-anterior"
"71048" "Left-T3-posterior"
"71049" "Left-Fusiform-gyrus"
"71050" "Left-Occipito-temporal-sulcus"
"71051" "Left-Collateral-sulcus"
"71052" "Left-Lingual-sulcus"
"71053" "Left-Parahippocampal-cortex"
"71054" "Left-Rhinal-cortex"
"71055" "Left-Postcentral-gyrus"
"71056" "Left-Postcentral-sulcus"
"71057" "Left-Superior-parietal-lobule-P1"
"71058" "Left-Supramarginal-anterior"
"71059" "Left-Supramarginal-posterior"
"71060" "Left-Angular-gyrus"
"71061" "Left-Intraparietal-sulcus"
"71062" "Left-Precuneus"
"71063" "Left-Marginal-branch-of-the-cingulate-sulcus"
"71064" "Left-Parieto-occipital-sulcus"
"71065" "Left-Anterior-occipital-sulcus-and-preoccipital-notch"
"71066" "Left-O3"
"71067" "Left-O2"
"71068" "Left-O1"
"71069" "Left-Occipital-pole"
"71070" "Left-Lingual-gyrus"
"71071" "Left-Calcarine-sulcus"
"71072" "Left-Cuneus"
"71073" "Left-Hippocampus-anterior"
"71074" "Left-Hippocampus-posterior"
"71075" "Left-Caudate-nucleus"
"71076" "Left-Nucleus-accumbens"
"71077" "Left-Cerebellar-cortex"
"72001" "Right-Frontal-pole"
"72002" "Right-Orbito-frontal-cortex"
"72003" "Right-Gyrus-rectus"
"72004" "Right-F3-Pars-Orbitalis"
"72005" "Right-F3-Pars-triangularis"
"72006" "Right-F3-pars-opercularis"
"72007" "Right-Inferior-frontal-sulcus"
"72008" "Right-F2-rostral"
"72009" "Right-F2-caudal"
"72010" "Right-Middle-frontal-sulcus"
"72011" "Right-SFS-rostral"
"72012" "Right-SFS-caudal"
"72013" "Right-F1-mesial-prefrontal"
"72014" "Right-PreSMA"
"72015" "Right-SMA"
"72016" "Right-F1-lateral-prefrontal"
"72017" "Right-F1-lateral-premotor"
"72018" "Right-Subcallosal-area"
"72019" "Right-Precentral-sulcus-inferior-part"
"72020" "Right-Precentral-sulcus-superior-part"
"72021" "Right-Precentral-gyrus-head-face"
"72022" "Right-Precentral-gyrus-upper-limb"
"72023" "Right-Central-sulcus-head-face"
"72024" "Right-Central-sulcus-upper-limb"
"72025" "Right-Paracentral-lobule"
"72026" "Right-Central-operculum"
"72027" "Right-Parietal-operculum"
"72028" "Right-Anterior-cingulate-cortex"
"72029" "Right-Middle-cingulate-cortex-anterior-part"
"72030" "Right-Middle-cingulate-cortex-posterior-part"
"72031" "Right-Posterior-cingulate-cortex-dorsal"
"72032" "Right-Posterior-cingulate-cortex-retrosplenial-gyrus"
"72033" "Right-Insula-gyri-brevi"
"72034" "Right-Insula-gyri-longi"
"72035" "Right-Temporal-pole"
"72036" "Right-T1-planum-polare"
"72037" "Right-Gyrus-of-Heschl"
"72038" "Right-T1-planum-temporale"
"72039" "Right-T1-lateral-anterior"
"72040" "Right-T1-lateral-posterior"
"72041" "Right-STS-anterior"
"72042" "Right-STS-posterior"
"72043" "Right-ITS-anterior"
"72044" "Right-ITS-posterior"
"72045" "Right-T2-anterior"
"72046" "Right-T2-posterior"
"72047" "Right-T3-anterior"
"72048" "Right-T3-posterior"
"72049" "Right-Fusiform-gyrus"
"72050" "Right-Occipito-temporal-sulcus"
"72051" "Right-Collateral-sulcus"
"72052" "Right-Lingual-sulcus"
"72053" "Right-Parahippocampal-cortex"
"72054" "Right-Rhinal-cortex"
"72055" "Right-Postcentral-gyrus"
"72056" "Right-Postcentral-sulcus"
"72057" "Right-Superior-parietal-lobule-P1"
"72058" "Right-Supramarginal-anterior"
"72059" "Right-Supramarginal-posterior"
"72060" "Right-Angular-gyrus"
"72061" "Right-Intraparietal-sulcus"
"72062" "Right-Precuneus"
"72063" "Right-Marginal-branch-of-the-cingulate-sulcus"
"72064" "Right-Parieto-occipital-sulcus"
"72065" "Right-Anterior-occipital-sulcus-and-preoccipital-notch"
"72066" "Right-O3"
"72067" "Right-O2"
"72068" "Right-O1"
"72069" "Right-Occipital-pole"
"72070" "Right-Lingual-gyrus"
"72071" "Right-Calcarine-sulcus"
"72072" "Right-Cuneus"
"72073" "Right-Hippocampus-anterior"
"72074" "Right-Hippocampus-posterior"
"72075" "Right-Caudate-nucleus"
"72076" "Right-Nucleus-accumbens"
"72077" "Right-Cerebellar-cortex"
</VALUE_LABEL_DTABLE>

I added it to the NIFTI header using

3drefit -labeltable VEP_atlas_AFNI.lt aparc+aseg+vep.nii 

the parcel names are displayed correctly, but the there are only two colors shown, one for grey and the other for white matter.

I tried MakeColorMap -in VepFreeSurferColorLutClean.txt -prefix aparc+aseg+vep with VepFreeSurferColorLutClean.txt looking like

#No. Label Name:                            R   G   B   A
0   Unknown                                 0   0   0   0
1   Left-Cerebral-Exterior                  70  130 180 0
2   Left-Cerebral-White-Matter              245 245 245 0
3   Left-Cerebral-Cortex                    205 62  78  0
4   Left-Lateral-Ventricle                  120 18  134 0
5   Left-Inf-Lat-Vent                       196 58  250 0
6   Left-Cerebellum-Exterior                0   148 0   0
7   Left-Cerebellum-White-Matter            220 248 164 0
8   Left-Cerebellum-Cortex                  230 148 34  0
9   Left-Thalamus                           0   118 14  0
10  Left-Thalamus-Proper                    0   118 14  0
11  Left-Caudate                            122 186 220 0
12  Left-Putamen                            236 13  176 0
13  Left-Pallidum                           12  48  255 0
14  3rd-Ventricle                           204 182 142 0
15  4th-Ventricle                           42  204 164 0
16  Brain-Stem                              119 159 176 0
17  Left-Hippocampus                        220 216 20  0
...

I placed the segmentation file and the corresponding nimal.cmap file (with the same name) in the same folder, but the colors in AFNI did not update. Is there a way to make the AFNI GUI automatically display the LUT colors?

Thanks

[dglen]

The afni and suma GUIs have different ways to create and use colormaps. Which are you trying to do here? The labeltable in volumes is mostly used for mapping labels with indices. The color is not used inside the dataset for afni, but a related color mapping can be loaded separately. The colors can be loaded through the colorbar menu. Right-click over the 'OLay' and select Read in palette. It's best to specify 256 colors. If you want to use other prepared color bars, you can switch among loaded color maps by right clicking on the color bar.

suma has some other options for color mapping, particularly for surfaces. With datasets mapped to the surface, you can control that with color mappings set to direct to force specific colors. You can use the "New" button to load a new colormap, and switch color maps with the "Cmp" button.

[zhengchencai]

Thanks. I am trying to make it work in the AFNI GUI. I would like the colormap to load automatically rather than having to change it manually each time. The idea is similar to aseg_REN, where AFNI automatically loads the correct colors and displays each parcel with a distinctive color. In my case, even if I try different color maps the segmentation still only show just two colors, one for grey and one for white matter. I wonder if this is because I added 70000 base value to labels of the grey matter segmentation.

[dglen]

You are running into a couple issues here. First, by default, the colormaps are limited to separating the overlay data into 256 colors. This can be extended to 2048 by calling afni with the -XXXnpane 2048 option one time.

Continuous colormaps are used for most datasets, but for datasets with parcellations of ROIs, you will want to use an integral colormap, like the ROI_256 color map. You can tell AFNI to show the dataset with integral color maps with

 3drefit -cmap INT_CMAP test70000+orig

A third set of problems is scaling the data to match the range in a useful way. With a max of around 70,000, the range is outside the signed integer range that has a maximum allowable value of 32767, so a floating point value would be required. Even with floating point, the range selector would need to be set to the maximum value. The default 256 divisions would distinguish colors in 70000/256 = 273, so 273 indices would get the same color, covering many of the subcortical regions. That gets divided by 8 for the maximum 2048 divisions.

This is all to say you are likely better off renumbering or ranking the dataset to make better use of color bars. That's how we handle the similar datasets in the FreeSurfer output.

[zhengchencai]

Thanks Daniel, indeed it was the value range issue. I renumbered them to < 256, it works.