[Brains-users] Segmentation trouble
Ronald Pierson
ronald at psychiatry.uiowa.edu
Wed Aug 23 09:56:09 PDT 2006
Here is a script I use (attached). You run it in the ACPC directory,
giving it simply the image name. You need to also have Talairach
bounds. You may need to modify it to work on your system.
One of the problems is that sometimes the fat, arterial flow, etc. are
so bright, that the intensities of the main brain tissue occupies only a
small part of the dynamic range of the image. This script looks for the
intensity of the image inside the brain, then brightens it up so that
that intensity range is in more useful. Everything above a certain
intensity is clipped to 255.
This script loads your image, loads the talairach paramters, creates a
mask of the brain box (interior of the brain, certain to not include
skull) and limits it to the occ. and parietal regions (to avoid the
middle cerebral artery, among others). It then finds the maximum
intensity in that region, adds 20 to it, and uses that number as a
cutoff. (you can change the "20" to something else, but it seemed to
work well for me). Above that number, the image will be pegged to 255.
Everything below that number will be spread out between 0 and 255.
This is probably a low-tech hack, but it has worked pretty nicely to
save some scans. A better step would be to do this on the original 16
bit or floating point image to avoid truncation effects. Or, save a
floating point resampled image, to be turned into a histogram-clipped 8-
bit image. The best would probably be to do a histogram-equalization
routine. Not sure it would really make any difference to the final
results, though.
Let me know how it works, and if someone has something better that is
easily available.
Ron
On Wed, 2006-08-23 at 14:03 +0200, Kevin Berne wrote:
> 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 t
hi
> 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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>
--
Ronald Pierson <ronald at psychiatry.uiowa.edu>
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