[Brains-users] Segmentation trouble
Kevin Berne
outerheaven23 at web.de
Wed Aug 23 05:03:39 PDT 2006
Hello,
After trying to run Brains2 on Cygwin some time ago (and failing to properly to do so), we have installed a Linux sytem and got Brains2 to run on it. Sadly, after completing the resampling and fitting of T1 and T2 (coregistration), I again tried the segmantation process, which failed again displaying the same error message it did under Cygwin some months ago. It reads "error accessing non-vacuous array tree". As I understood it back then, and as some members of the forum users suggested, this was due to dark images. This I can verify, and have since employed the thresholding algorithm I was given through this forum to enhance the almost completely black T1 images to a nice brightness level (which never worked under Cygwin). Nevertheless, the aforementioned error keeps blocking up, preventing me from continuing. Not even deactivating the manual venous blood trace under "blood method" in the segmentation dialog box and just chosing "Image T1 top 250 voxels" below makes the thi
ng work. My question is, how can I perhaps brighten up the T2 (Image math/add does not work...), since they are still quite dark, can this even be the cause of the problem, or could the problem also be the manual venous blood trace (or would this result in another kind of error message)? Below I have posted a quite extensive coverage of the faulty segmentation process, in the hope that someone knows how I can get this to work, since I have been trying to get past this point for much too many months already now. So, any kind of help would be much appreciated.
Thank you very much already,
Kevin Berne
ZI Mannheim
Germany
Brains2 <-> Itk Conversion library /opt/brains2/lib/libconnectBrainsItkTcl.so activated
brains2% b2 load image /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/psm_8001_10_Unknown.hdr
Object loaded with filter: strictAnalyze75
b2 load image /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/T2_resampled.hdr
Object loaded with filter: strictAnalyze75
b2 load talairach-parameters /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/Talairach.bnd
Object loaded with filter: brains2
b2 load talairach-box /opt/brains2/bin/talairach/brain_box
Object loaded with filter: brains1
b2 convert talairach-box to mask talbox1 talpar1
b2 destroy talairach-parameters talpar1
b2 destroy talairach-box talbox1
b2 load roi /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/root/l_seg_vb.zroi
Object loaded with filter: brains2
b2 convert roi to mask r1 interpolate= False
b2 destroy roi r1
b2 load roi /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/root/r_seg_vb.zroi
Object loaded with filter: brains2
b2 convert roi to mask r2 interpolate= False
b2 destroy roi r2
b2 or masks m2 m3
b2 destroy mask m2
b2 destroy mask m3
Remark: min gm plugs == 4000
Remark: min wm plugs == 2000
Remark: min csf plugs == 200
b2 generate class-plugs {i1 i2} {gm wm csf} {{80.186111 113.979065 30.087282 10.8} {117.773056 84.270554 222.857208 68.8}} m1 r= psm_8001 n= 4000 c= 0.85 p= 0.10 mo= 2.5 vo= 10.0 ps= 2.0 dx= 1 dy= 1 dz= 1 gm= 4000 wm= 2000 csf= 200 pb= m4
Diagnostic: bk_generateClassPlugs entered.
Diagnostic: pv_plugCluster entered. numClasses == 3
Diagnostic: plug dimensions = 2 x 2 x 2, plug volume = 8.000 voxels
Rand seed 1156331561
Rand Array 0 1156331561
Diagnostic: Random Number generator seed = 1156331561
Diagnostic: enclosing box is 76..178 x 87..191 x 15..168
Diagnostic: brain mask has 699274 voxels
Diagnostic: Image set plug variance table: 0 (10.800)
Diagnostic: Image set plug variance table: 1 (68.800)
Diagnostic: chunk_z 15..168
Diagnostic: chunk_y 87..191
Diagnostic: chunk_x 76..178
Diagnostic: initial count1 = 702253 , oldcount1 = 699274
Diagnostic: Coverage [3] = 0.850
Diagnostic: max_points = 119999 , numplugs = 4017
Diagnostic: count1 = 702253, count = 0, sumplugs = 4017
Diagnostic: desired = 4017, pick_from = 174, band = 5
Diagnostic: desired = 2969, pick_from = 174, band = 20
Diagnostic: HARVESTED 4111 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 44.000 83.062
Class 2: 82.000 51.188
Class 3: 44.000 83.062
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 4078
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 123.345 centers[1][2] = 49.009
Diagnostic: NC[2] = 33
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 26.091 centers[2][2] = 120.330
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 123.345 26.091 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 49.009 120.330 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 1 not yet sufficient.
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 4111 class_count[0] = 33
plug_count[2] = 4111 class_count[2] = 0
Diagnostic: count1 = 702253, count = 4111, sumplugs = 8034
Diagnostic: desired = 3923, pick_from = 179, band = 5
Diagnostic: desired = 3073, pick_from = 179, band = 24
Diagnostic: desired = 125, pick_from = 179, band = 26
Diagnostic: HARVESTED 10305 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 46.000 82.500
Class 2: 88.000 50.250
Class 3: 46.000 82.500
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 10213
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 122.300 centers[1][2] = 49.818
Diagnostic: NC[2] = 92
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 27.913 centers[2][2] = 119.067
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 122.300 27.913 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 49.818 119.067 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 10305 class_count[0] = 92
plug_count[2] = 10305 class_count[2] = 0
Diagnostic: count1 = 702253, count = 10305, sumplugs = 12051
Diagnostic: desired = 1746, pick_from = 402, band = 5
Diagnostic: desired = 1503, pick_from = 402, band = 36
Diagnostic: desired = 300, pick_from = 402, band = 45
Diagnostic: HARVESTED 12958 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 46.000 82.500
Class 2: 88.000 50.250
Class 3: 46.000 82.500
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 12822
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.971 centers[1][2] = 50.025
Diagnostic: NC[2] = 136
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 28.132 centers[2][2] = 118.301
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.971 28.132 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.025 118.301 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 12958 class_count[0] = 136
plug_count[2] = 12958 class_count[2] = 0
Diagnostic: count1 = 702253, count = 12958, sumplugs = 16068
Diagnostic: desired = 3110, pick_from = 225, band = 5
Diagnostic: desired = 2844, pick_from = 225, band = 59
Diagnostic: desired = 426, pick_from = 225, band = 70
Diagnostic: HARVESTED 17569 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 82.500
Class 2: 81.500 50.250
Class 3: 35.167 82.500
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 17351
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.533 centers[1][2] = 50.350
Diagnostic: NC[2] = 218
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 28.050 centers[2][2] = 115.939
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.533 28.050 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.350 115.939 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 17569 class_count[0] = 218
plug_count[2] = 17569 class_count[2] = 0
Diagnostic: count1 = 702253, count = 17569, sumplugs = 20085
Diagnostic: desired = 2516, pick_from = 279, band = 5
Diagnostic: desired = 2445, pick_from = 279, band = 178
Diagnostic: desired = 35, pick_from = 279, band = 181
Diagnostic: HARVESTED 20912 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 74.688
Class 2: 81.500 37.229
Class 3: 35.167 74.688
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 20630
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.227 centers[1][2] = 50.579
Diagnostic: NC[2] = 282
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 28.759 centers[2][2] = 114.148
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.227 28.759 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.579 114.148 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 20912 class_count[0] = 282
plug_count[2] = 20912 class_count[2] = 0
Diagnostic: count1 = 702253, count = 20912, sumplugs = 24102
Diagnostic: desired = 3190, pick_from = 220, band = 5
Diagnostic: desired = 3173, pick_from = 220, band = 220
Diagnostic: HARVESTED 21446 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 74.688
Class 2: 81.500 37.229
Class 3: 35.167 74.688
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 21143
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.163 centers[1][2] = 50.640
Diagnostic: NC[2] = 303
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 29.017 centers[2][2] = 113.641
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.163 29.017 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.640 113.641 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 21446 class_count[0] = 303
plug_count[2] = 21446 class_count[2] = 0
Diagnostic: count1 = 702253, count = 21446, sumplugs = 28119
Diagnostic: desired = 6673, pick_from = 105, band = 5
Diagnostic: desired = 6671, pick_from = 105, band = 105
Diagnostic: HARVESTED 21480 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 74.688
Class 2: 81.500 37.229
Class 3: 35.167 74.688
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 21174
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.148 centers[1][2] = 50.653
Diagnostic: NC[2] = 306
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 29.016 centers[2][2] = 113.561
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.148 29.016 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.653 113.561 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 21480 class_count[0] = 306
plug_count[2] = 21480 class_count[2] = 0
Diagnostic: count1 = 702253, count = 21480, sumplugs = 32136
Diagnostic: desired = 10656, pick_from = 65, band = 5
Diagnostic: desired = 10656, pick_from = 65, band = 65
Diagnostic: HARVESTED 21504 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 74.688
Class 2: 81.500 37.229
Class 3: 35.167 74.688
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 21189
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.141 centers[1][2] = 50.662
Diagnostic: NC[2] = 315
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 29.178 centers[2][2] = 112.953
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.141 29.178 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.662 112.953 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 21504 class_count[0] = 315
plug_count[2] = 21504 class_count[2] = 0
Diagnostic: count1 = 702253, count = 21504, sumplugs = 36153
Diagnostic: desired = 14649, pick_from = 47, band = 5
Diagnostic: desired = 14646, pick_from = 47, band = 47
Diagnostic: HARVESTED 21519 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 74.688
Class 2: 81.500 37.229
Class 3: 35.167 74.688
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 21201
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.137 centers[1][2] = 50.668
Diagnostic: NC[2] = 318
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 29.176 centers[2][2] = 112.684
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.137 29.176 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.668 112.684 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 21519 class_count[0] = 318
plug_count[2] = 21519 class_count[2] = 0
Diagnostic: count1 = 702253, count = 21519, sumplugs = 40170
Diagnostic: desired = 18651, pick_from = 37, band = 5
Diagnostic: desired = 18650, pick_from = 37, band = 37
Diagnostic: HARVESTED 21529 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 74.688
Class 2: 81.500 37.229
Class 3: 35.167 74.688
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 21209
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.128 centers[1][2] = 50.672
Diagnostic: NC[2] = 320
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 29.188 centers[2][2] = 112.687
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.128 29.188 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.672 112.687 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 21529 class_count[0] = 320
plug_count[2] = 21529 class_count[2] = 0
Diagnostic: count1 = 702253, count = 21529, sumplugs = 44187
Diagnostic: desired = 22658, pick_from = 30, band = 5
Diagnostic: desired = 22657, pick_from = 30, band = 30
Diagnostic: HARVESTED 21534 plugs in chunk 15..168 x 87..191 x 76..178.
Table of initial centers:
Class 1: 80.186 117.773
Class 2: 113.979 84.271
Class 3: 30.087 222.857
Diagnostic: ipl_KMNS produced IFAULT = 1
Table of initial centers:
Class 1: 35.167 74.688
Class 2: 81.500 37.229
Class 3: 35.167 74.688
Diagnostic: ipl_KMNS produced IFAULT = 1
Warning Diagnostic: =====> map of class mean order statistics failed to resolve the desired number of classes!
Diagnostic: NC[1] = 21213
Diagnostic: WSS[1] = 0.000 : 0.000
Diagnostic: Center Table
centers[1][1] = 121.128 centers[1][2] = 50.674
Diagnostic: NC[2] = 321
Diagnostic: WSS[2] = 0.000 : 0.000
Diagnostic: Center Table
centers[2][1] = 29.174 centers[2][2] = 112.649
Diagnostic: NC[3] = 0
Diagnostic: WSS[3] = 0.000 : nan
Diagnostic: Center Table
centers[3][1] = 0.000 centers[3][2] = 0.000
Image 0: Centers: 121.128 29.174 0.000
Image 0: Permutation: 2 1 3
Image 1: Centers: 50.674 112.649 0.000
Image 1: Permutation: 3 1 2
Diagnostic: =====> class 0 labeling according to image 1 differs from first image.
Diagnostic: =====> class 2 labeling according to image 1 differs from first image.
box_flag[1] = 1
box_flag[0] = 0
box_flag[2] = 0
Class 0 not yet sufficient.
Class 2 not yet sufficient.
plug_count[1] = 4111 class_count[1] = 4078
plug_count[0] = 21534 class_count[0] = 321
plug_count[2] = 21534 class_count[2] = 0
bloodMode == 0, blood rule image == 0
Writing output plug masks.
b2 save mask /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/grey_plugs.mask brains2 m5
b2 save mask /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/white_plugs.mask brains2 m6
b2 save mask /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/csf_plugs.mask brains2 m7
b2 save mask /home/morpho/MR_Volumetrie_Studie/BPD_Patientinnen/psm_8001/10_ACPC/blood_plugs.mask brains2 m8
b2 generate class-model {T1 T2} {i1 i2} {gm wm csf vb} {m5 m6 m7 m8} m1 hist-eq= 1 tg= 0.0 ts= 0.0 x= 1 y= 1 z= 1 xx= 1 yy= 1 zz= 1 xy= 1 xz= 1 yz= 1
Diagnostic: bk_generateClassModel entered.
SIMPLE_ERROR: error accessing non-vacuous array tree: 0-th PLUG MASK WAS EMPTY. Module: /scratch/hjohnson/src/brains2/src/iplObject/obTissueClass.cxx Function: bk_generateClassModel Line: 4107 Code: 123456789
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