Node disappear following labelconvert

1

Dear Mrtrixers,
I have been trying to generate a custom node using “labelconvert”. I have created label file and custom lut_out file (default-ha).
However, it produces file

Fig_1_Missing_Nodes
Fig_1_Missing_Nodes.jpg1915×1056 365 KB
that has many missed many nodes. Would you please help troubleshooting this problem?
Here I copied the content of default-ha.txt file.

Kind regards
Md Mamun Al Amin
QBI, UQ, Brisbane, Australia

0 ??? Unknown 0 0 0 0

1 L.BSTS ctx-lh-bankssts 25 100 40 255
2 L.CACG ctx-lh-caudalanteriorcingulate 125 100 160 255
3 L.CMFG ctx-lh-caudalmiddlefrontal 100 25 0 255
4 L.CU ctx-lh-cuneus 220 20 100 255
5 L.EC ctx-lh-entorhinal 220 20 10 255
6 L.FG ctx-lh-fusiform 180 220 140 255
7 L.IPG ctx-lh-inferiorparietal 220 60 220 255
8 L.ITG ctx-lh-inferiortemporal 180 40 120 255
9 L.ICG ctx-lh-isthmuscingulate 140 20 140 255
10 L.LOG ctx-lh-lateraloccipital 20 30 140 255
11 L.LOFG ctx-lh-lateralorbitofrontal 35 75 50 255
12 L.LG ctx-lh-lingual 225 140 140 255
13 L.MOFG ctx-lh-medialorbitofrontal 200 35 75 255
14 L.MTG ctx-lh-middletemporal 160 100 50 255
15 L.PHIG ctx-lh-parahippocampal 20 220 60 255
16 L.PaCG ctx-lh-paracentral 60 220 60 255
17 L.POP ctx-lh-parsopercularis 220 180 140 255
18 L.POR ctx-lh-parsorbitalis 20 100 50 255
19 L.PTR ctx-lh-parstriangularis 220 60 20 255
20 L.PCAL ctx-lh-pericalcarine 120 100 60 255
21 L.PoCG ctx-lh-postcentral 220 20 20 255
22 L.PCG ctx-lh-posteriorcingulate 220 180 220 255
23 L.PrCG ctx-lh-precentral 60 20 220 255
24 L.PCU ctx-lh-precuneus 160 140 180 255
25 L.RACG ctx-lh-rostralanteriorcingulate 80 20 140 255
26 L.RMFG ctx-lh-rostralmiddlefrontal 75 50 125 255
27 L.SFG ctx-lh-superiorfrontal 20 220 160 255
28 L.SPG ctx-lh-superiorparietal 20 180 140 255
29 L.STG ctx-lh-superiortemporal 140 220 220 255
30 L.SMG ctx-lh-supramarginal 80 160 20 255
31 L.FP ctx-lh-frontalpole 100 0 100 255
32 L.TP ctx-lh-temporalpole 70 70 70 255
33 L.TTG ctx-lh-transversetemporal 150 150 200 255
34 L.IN ctx-lh-insula 255 192 32 255

35 L.CER Left-Cerebellum-Cortex 230 148 34 255

36 L.TH Left-Thalamus-Proper 0 118 14 255
37 L.CA Left-Caudate 122 186 220 255
38 L.PU Left-Putamen 236 13 176 255
39 L.PA Left-Pallidum 12 48 255 255
40 L.PSb Left-parasubiculum 175 175 75 255
41 L.PrS Left-presubiculum 64 0 64 255
42 L.Sub Left-subiculum 0 0 255 255
43 L.C1 Left-CA1 255 0 0 255
44 L.C2 Left-CA2 128 128 255 255
45 L.C3 Left-CA3 0 128 0 255
46 L.C4 Left-CA4 196 160 128 255
47 L.DG Left-GC-DG 32 200 255 255
48 L.HT Left-HATA 128 255 128 255
49 L.FB Left-fimbria 204 153 204 255
50 L.ML Left-molecular_layer_HP 128 0 0 255
51 L.hf Left-hippocampal_fissure 128 32 255 255
52 L.ht Left-HP_tail 170 170 255 255
53 L.Ln Left_Lateral-nucleus 72 132 181 255
54 L.Bn Left_Basal-nucleus 207 63 79 255
55 L.CN Left_Central-nucleus 197 60 248 255
56 L.Con Left_Cortical-nucleus 221 249 166 255
57 L.ABnR Left_Accessory-Basal-nucleus 232 146 35 255
58 L.CATR Left_Corticoamygdaloid-trans 20 60 120 255
59 L.Aat Left_Anterior-amygdaloid-are 250 250 0 255
60 L.Pn Left_Paralaminar-nucleus 45 205 165 255

61 L.AC Left-Accumbens-area 255 165 0 255

62 R.TH Right-Thalamus-Proper 0 118 14 255
63 R.CA Right-Caudate 122 186 220 255
64 R.PU Right-Putamen 236 13 176 255
65 R.PA Right-Pallidum 13 48 255 255
66 R.PSb Right-parasubiculum 175 175 75 255
67 R.PrS Right-presubiculum 64 0 64 255
68 R.Sub Right-subiculum 0 0 255 255
69 R.C1 Right-CA1 255 0 0 255
70 R.C2 Right-CA2 128 128 255 255
71 R.C3 Right-CA3 0 128 0 255
72 R.C4 Right-CA4 196 160 128 255
73 R.DG Right-GC-DG 32 200 255 255
74 R.HT Right-HATA 128 255 128 255
75 R.FB Right-fimbria 204 153 204 255
76 R.ML Right-molecular_layer_HP 128 0 0 255
77 R.hf Right-hippocampal_fissure 128 32 255 255
78 R.ht Right-HP_tail 170 170 255 255
79 R.Ln Right_Lateral-nucleus 72 132 181 255
80 R.Bn Right_Basal-nucleus 207 63 79 255
81 R.CN Right_Central-nucleus 197 60 248 255
82 R.Con Right_Cortical-nucleus 221 249 166 255
83 R.ABnR Right_Accessory-Basal-nucleus 232 146 35 255
84 R.CATR Right_Corticoamygdaloid-trans 20 60 120 255
85 R.Aat Right_Anterior-amygdaloid-are 250 250 0 255
86 R.Pn Right_Paralaminar-nucleus 45 205 165 255

87 R.AC Right-Accumbens-area 255 165 0 255

88 R.BSTS ctx-rh-bankssts 25 100 40 255
89 R.CACG ctx-rh-caudalanteriorcingulate 125 100 160 255
90 R.CMFG ctx-rh-caudalmiddlefrontal 100 25 0 255
91 R.CU ctx-rh-cuneus 220 20 100 255
92 R.EC ctx-rh-entorhinal 220 20 10 255
93 R.FG ctx-rh-fusiform 180 220 140 255
94 R.IPG ctx-rh-inferiorparietal 220 60 220 255
95 R.ITG ctx-rh-inferiortemporal 180 40 120 255
96 R.ICG ctx-rh-isthmuscingulate 140 20 140 255
97 R.LOG ctx-rh-lateraloccipital 20 30 140 255
98 R.LOFG ctx-rh-lateralorbitofrontal 35 75 50 255
99 R.LG ctx-rh-lingual 225 140 140 255
100 R.MOFG ctx-rh-medialorbitofrontal 200 35 75 255
101 R.MTG ctx-rh-middletemporal 160 100 50 255
102 R.PHIG ctx-rh-parahippocampal 20 220 60 255
103 R.PaCG ctx-rh-paracentral 60 220 60 255
104 R.POP ctx-rh-parsopercularis 220 180 140 255
105 R.POR ctx-rh-parsorbitalis 20 100 50 255
106 R.PTR ctx-rh-parstriangularis 220 60 20 255
107 R.PCAL ctx-rh-pericalcarine 120 100 60 255
108 R.PoCG ctx-rh-postcentral 220 20 20 255
109 R.PCG ctx-rh-posteriorcingulate 220 180 220 255
110 R.PrCG ctx-rh-precentral 60 20 220 255
111 R.PCU ctx-rh-precuneus 160 140 180 255
112 R.RACG ctx-rh-rostralanteriorcingulate 80 20 140 255
113 R.RMFG ctx-rh-rostralmiddlefrontal 75 50 125 255
114 R.SFG ctx-rh-superiorfrontal 20 220 160 255
115 R.SPG ctx-rh-superiorparietal 20 180 140 255
116 R.STG ctx-rh-superiortemporal 140 220 220 255
117 R.SMG ctx-rh-supramarginal 80 160 20 255
118 R.FP ctx-rh-frontalpole 100 0 100 255
119 R.TP ctx-rh-temporalpole 70 70 70 255
120 R.TTG ctx-rh-transversetemporal 150 150 200 255
121 R.IN ctx-rh-insula 255 192 32 255

122 R.CER Right-Cerebellum-Cortex 230 148 34 255

2

When you say that the parcellation is “missing nodes”, are you referring only to the contents of the node list in the sidebar in mrview? I don’t quite know what’s going on there. Generally when one describes “missing nodes” in the context of labelconvert, the intended meaning is that there are voxels with non-zero value in the input image that should also have non-zero value in the output image, but those voxels are instead zero, i.e. the node “disappears”.

3

Hi Rob
I understand where the problem was. Basically, I had ROIs in the both hemisphere with same number. So, they were conflicting. I fixed them. I had created entirely an new Lut file and a target lookup table.
I appreciate your help.

Kind regards
Mamun