Hi experts,

I was just wondering if was possible to change the minimum and maximum values of the edge's colormap and have the edges reflect this new color?

Currently, my legend of the edge colors shows values that range from -4 to -2, which reflects my edge values. However, I would like to have the legend of the edge colors range from -5 to 5 and that the color of the edges would match this new legend of edge colors.

I tried Option > Colormap Editor to adjust min/max value manually, this adjusts the legend of the edge color, but does not adjust the actual colors of the edges to match the new legend.

I also tried to save the new colormap with a new min/max value using the Colormap Editor and load it by selecting Custom Matrix in Edge Options. However, I get an error stating that 'The size of the color matrix does not match the edge of the file'.

Thanks!,
Ekarin P.

Hi, 

The Option > Colormap Editor is only for the volume to surface mapping. To fix the edge color range, you have to modify the codes of BrainNet.m

in about line 420, the original codes are:
"tmp = surf.cylinder(:,5);
if max(tmp) ~=min(tmp)
k = 63 /(max(tmp)-min(tmp));
b = 64 - k*max(tmp);
else
k = 0;
b = 64;
end
tmp = round(tmp * k + b);
tmp(tmp < 1) = 1;
tmp(tmp > 64) = 64;
surf.cylinder(:,5) = tmp;"

modify them as:
"tmp = surf.cylinder(:,5);
if max(tmp) ~=min(tmp)
k = 63/(10) ;
b = 64 - k*5;
else
k = 0;
b = 64;
end
tmp = round(tmp * k + b);
tmp(tmp < 1) = 1;
tmp(tmp > 64) = 64;
surf.cylinder(:,5) = tmp;"

After these changes, Please ignore the numbers of colorbar in the final figure. Just ps it to -5 and 5, because at least four other places have to be modified to change the number. It is not necessary. 

Best,
Mingrui

I am trying to create a custom colormap but I am getting an error: 'The size of the color matrix does not match the edge of the file'.

I have tried to figure out how to create this file by first taking an existing colormap and saving it and then trying to use it again but I am getting then this same error.

So my question is, how should this custom colormap file look like?

Thank you in advance,
Noora

Hi,

The color matrix should be the same size as the edge matrix. The values in this matrix indicate different colors of the colormap. 

Best,
Mingrui

So if I have a edge matrix 116*116, I should have a matrix 116*3 for color matrix?

I have tried to create a .txt file in this way
[x1 x2 x3; y1 y2 y3....n1 n2 n3] but it wont work. Please specify how should the file be or if you can give me an example of custom colormap file that works. Thank you!

Noora

No, the custom matrix should be 166*116, in which each value corresponding to the color index of each edge.

BrainNet Viewer is not ready to input a custom colormap for edges. To do so, you have to modify the codes. 

For example, the values in your custom matrix ranges from 0 to 1, and you want to use a colormap that gradually changes from white to red. Please edit BrainNet_Option.m

in about line 1286, you may find "EC.edg.CM=jet;"

replace it with "EC.edg.CM = [linspace(255,255,64);linspace(255,0,64);linspace(255,0,64)]'/255;"

The first number in function linespace represents the color for lowest value (here, [255,255,255] means the RGB value of white) and the second number means the color for highest value ([255,0,0] for red).

Mingrui

Thanks for the reply!
This has helped me further and I am much closer to the solution by changing values in BrainNet_Option.m file.

I have changed values for "EC.edg.CM=[0.655172413800000 1 0.344827586200000;.....;0.724137931000000 1 0.275862069000000]"
to correspond each value for 1..116

-Noora

Hopping on this 4-year-old thread because I have a similar issue...

I managed to use the code to create a custom colormap, and it shows up in the colorbar/legend beautifully, but the actual edge colors are not matching the full range of colors in the colorbar. The colorbar ranges from purple to yellow, and all the lines are purple despite differing values. For example, the legend shows that edges with a value of 5 should be yellow, but they are purple in the actual figure. Is there another option I need to change, either in the GUI or in the code?

Thanks!

Hi, Could you please attach your files, option setting, and custom colormap, so that we can have a test. 

Mingrui
Originally posted by kara:

Here is the edit I made to BrainNet_Option.m:

EC.edg.CM=[0.050383 0.029803 0.527975
0.063536 0.028426 0.533124
0.075353 0.027206 0.538007
0.086222 0.026125 0.542658
0.096379 0.025165 0.547103
0.105980 0.024309 0.551368
0.115124 0.023556 0.555468
0.123903 0.022878 0.559423
0.132381 0.022258 0.563250
0.140603 0.021687 0.566959
0.148607 0.021154 0.570562
0.156421 0.020651 0.574065
0.164070 0.020171 0.577478
0.171574 0.019706 0.580806
0.178950 0.019252 0.584054
0.186213 0.018803 0.587228
0.193374 0.018354 0.590330
0.200445 0.017902 0.593364
0.207435 0.017442 0.596333
0.214350 0.016973 0.599239
0.221197 0.016497 0.602083
0.227983 0.016007 0.604867
0.234715 0.015502 0.607592
0.241396 0.014979 0.610259
0.248032 0.014439 0.612868
0.254627 0.013882 0.615419
0.261183 0.013308 0.617911
0.267703 0.012716 0.620346
0.274191 0.012109 0.622722
0.280648 0.011488 0.625038
0.287076 0.010855 0.627295
0.293478 0.010213 0.629490
0.299855 0.009561 0.631624
0.306210 0.008902 0.633694
0.312543 0.008239 0.635700
0.318856 0.007576 0.637640
0.325150 0.006915 0.639512
0.331426 0.006261 0.641316
0.337683 0.005618 0.643049
0.343925 0.004991 0.644710
0.350150 0.004382 0.646298
0.356359 0.003798 0.647810
0.362553 0.003243 0.649245
0.368733 0.002724 0.650601
0.374897 0.002245 0.651876
0.381047 0.001814 0.653068
0.387183 0.001434 0.654177
0.393304 0.001114 0.655199
0.399411 0.000859 0.656133
0.405503 0.000678 0.656977
0.411580 0.000577 0.657730
0.417642 0.000564 0.658390
0.423689 0.000646 0.658956
0.429719 0.000831 0.659425
0.435734 0.001127 0.659797
0.441732 0.001540 0.660069
0.447714 0.002080 0.660240
0.453677 0.002755 0.660310
0.459623 0.003574 0.660277
0.465550 0.004545 0.660139
0.471457 0.005678 0.659897
0.477344 0.006980 0.659549
0.483210 0.008460 0.659095
0.489055 0.010127 0.658534
0.494877 0.011990 0.657865
0.500678 0.014055 0.657088
0.506454 0.016333 0.656202
0.512206 0.018833 0.655209
0.517933 0.021563 0.654109
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0.557243 0.047331 0.643443
0.562738 0.051545 0.641509
0.568201 0.055778 0.639477
0.573632 0.060028 0.637349
0.579029 0.064296 0.635126
0.584391 0.068579 0.632812
0.589719 0.072878 0.630408
0.595011 0.077190 0.627917
0.600266 0.081516 0.625342
0.605485 0.085854 0.622686
0.610667 0.090204 0.619951
0.615812 0.094564 0.617140
0.620919 0.098934 0.614257
0.625987 0.103312 0.611305
0.631017 0.107699 0.608287
0.636008 0.112092 0.605205
0.640959 0.116492 0.602065
0.645872 0.120898 0.598867
0.650746 0.125309 0.595617
0.655580 0.129725 0.592317
0.660374 0.134144 0.588971
0.665129 0.138566 0.585582
0.669845 0.142992 0.582154
0.674522 0.147419 0.578688
0.679160 0.151848 0.575189
0.683758 0.156278 0.571660
0.688318 0.160709 0.568103
0.692840 0.165141 0.564522
0.697324 0.169573 0.560919
0.701769 0.174005 0.557296
0.706178 0.178437 0.553657
0.710549 0.182868 0.550004
0.714883 0.187299 0.546338
0.719181 0.191729 0.542663
0.723444 0.196158 0.538981
0.727670 0.200586 0.535293
0.731862 0.205013 0.531601
0.736019 0.209439 0.527908
0.740143 0.213864 0.524216
0.744232 0.218288 0.520524
0.748289 0.222711 0.516834
0.752312 0.227133 0.513149
0.756304 0.231555 0.509468
0.760264 0.235976 0.505794
0.764193 0.240396 0.502126
0.768090 0.244817 0.498465
0.771958 0.249237 0.494813
0.775796 0.253658 0.491171
0.779604 0.258078 0.487539
0.783383 0.262500 0.483918
0.787133 0.266922 0.480307
0.790855 0.271345 0.476706
0.794549 0.275770 0.473117
0.798216 0.280197 0.469538
0.801855 0.284626 0.465971
0.805467 0.289057 0.462415
0.809052 0.293491 0.458870
0.812612 0.297928 0.455338
0.816144 0.302368 0.451816
0.819651 0.306812 0.448306
0.823132 0.311261 0.444806
0.826588 0.315714 0.441316
0.830018 0.320172 0.437836
0.833422 0.324635 0.434366
0.836801 0.329105 0.430905
0.840155 0.333580 0.427455
0.843484 0.338062 0.424013
0.846788 0.342551 0.420579
0.850066 0.347048 0.417153
0.853319 0.351553 0.413734
0.856547 0.356066 0.410322
0.859750 0.360588 0.406917
0.862927 0.365119 0.403519
0.866078 0.369660 0.400126
0.869203 0.374212 0.396738
0.872303 0.378774 0.393355
0.875376 0.383347 0.389976
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0.881443 0.392529 0.383229
0.884436 0.397139 0.379860
0.887402 0.401762 0.376494
0.890340 0.406398 0.373130
0.893250 0.411048 0.369768
0.896131 0.415712 0.366407
0.898984 0.420392 0.363047
0.901807 0.425087 0.359688
0.904601 0.429797 0.356329
0.907365 0.434524 0.352970
0.910098 0.439268 0.349610
0.912800 0.444029 0.346251
0.915471 0.448807 0.342890
0.918109 0.453603 0.339529
0.920714 0.458417 0.336166
0.923287 0.463251 0.332801
0.925825 0.468103 0.329435
0.928329 0.472975 0.326067
0.930798 0.477867 0.322697
0.933232 0.482780 0.319325
0.935630 0.487712 0.315952
0.937990 0.492667 0.312575
0.940313 0.497642 0.309197
0.942598 0.502639 0.305816
0.944844 0.507658 0.302433
0.947051 0.512699 0.299049
0.949217 0.517763 0.295662
0.951344 0.522850 0.292275
0.953428 0.527960 0.288883
0.955470 0.533093 0.285490
0.957469 0.538250 0.282096
0.959424 0.543431 0.278701
0.961336 0.548636 0.275305
0.963203 0.553865 0.271909
0.965024 0.559118 0.268513
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0.970205 0.575028 0.258325
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0.977995 0.861432 0.142808
0.976265 0.868016 0.143351
0.974443 0.874622 0.144061
0.972530 0.881250 0.144923
0.970533 0.887896 0.145919
0.968443 0.894564 0.147014
0.966271 0.901249 0.148180
0.964021 0.907950 0.149370
0.961681 0.914672 0.150520
0.959276 0.921407 0.151566
0.956808 0.928152 0.152409
0.954287 0.934908 0.152921
0.951726 0.941671 0.152925
0.949151 0.948435 0.152178
0.946602 0.955190 0.150328
0.944152 0.961916 0.146861
0.941896 0.968590 0.140956
0.940015 0.975158 0.131326];

I've attached the node file as well. Will post other files in next messages (not sure if it's my computer or what, but I can't seem to attach more than one file). Not sure if this matters, but it's a double brain figure.

Edge file attached

Attached screenshot of the selected Edge options in the gui

Thank you!

Hi, 

There is an option to fix the colormap range for edges in the option panel. Please see attached pic for reference.
Originally posted by kara: