Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

VipT1BiasCorrection exits with error 111 on some data #2

Open
nsouedet opened this issue Feb 10, 2022 · 5 comments
Open

VipT1BiasCorrection exits with error 111 on some data #2

nsouedet opened this issue Feb 10, 2022 · 5 comments
Assignees
@nsouedet
Labels
bug Something isn't working

Comments

@nsouedet
Copy link
Contributor

Describe the bug
VipT1BiasCorrection ends with error 111 and many error messages.

To Reproduce
Steps to reproduce the behavior:

  1. Download files:

  2. Extract BB339F.zip and baseline_mri_BB336F.zip content

  3. In bv environment built on branch 5.0, run the command :

'VipT1BiasCorrection' '-i' 'BB339F.nii.gz' '-o' 'VIP_nobias_BB339F.nii.gz' '-field' 'VIP_biasfield_BB339F.nii.gz' '-wridge' 'whiteridge_BB339F.nii.gz' '-ename' 'edges_BB339F.nii.gz' '-vname' 'variance_BB339F.nii.gz' '-mname' 'mean_curvature_BB339F.nii.gz' '-hname' 'hfiltered_BB339F.nii.gz' '-Dcorrect' 'yes' '-Fwrite' 'yes' '-Wwrite' 'no' '-eWrite' 'no' '-vWrite' 'no' '-mWrite' 'no' '-hWrite' 'no' '-Kentropy' '1.0' '-Kcrest' '20.0' '-Kregul' '20.0' '-Koffset' '20.0' '-sampling' '16.0' '-Grid' '2' '-vp' '75' '-Last' 'auto (AC/PC Points needed)' '-Dkeep' '35.0' '-edges' '3' '-Cweight' 'T2' '-debug' 'no' '-dumb' 'yes' '-Points' 'BB339F.APC' '-Specie' 'Macaque'
  1. See standard output and error :
/casa/host/build/bin/VipT1BiasCorrection 
Command line
'VipT1BiasCorrection' '-i' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/BB339F.nii.gz' '-o' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/pre_analysis/VIP_nobias_BB339F.nii.gz' '-field' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/pre_analysis/VIP_biasfield_BB339F.nii.gz' '-wridge' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/pre_analysis/whiteridge_BB339F.nii.gz' '-ename' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/pre_analysis/edges_BB339F.nii.gz' '-vname' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/pre_analysis/variance_BB339F.nii.gz' '-mname' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/pre_analysis/mean_curvature_BB339F.nii.gz' '-hname' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/pre_analysis/hfiltered_BB339F.nii.gz' '-Dcorrect' 'yes' '-Fwrite' 'yes' '-Wwrite' 'no' '-eWrite' 'no' '-vWrite' 'no' '-mWrite' 'no' '-hWrite' 'no' '-Kentropy' '1.0' '-Kcrest' '20.0' '-Kregul' '20.0' '-Koffset' '20.0' '-sampling' '16.0' '-Grid' '2' '-vp' '75' '-Last' 'auto (AC/PC Points needed)' '-Dkeep' '35.0' '-edges' '3' '-Cweight' 'T2' '-debug' 'no' '-dumb' 'yes' '-Points' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/BB339F.APC' '-Specie' 'Macaque'
Output
3D field regularization
little_opening_size=0.900003

Reading AC, PC, IH coordinates: /home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/BB339F/anatomical_mri/default_acquisition/BB339F.APC
Reading Coordinate file (AC, PC...)
Anterior commissure: 122 31 78
Posterior commissure: 121 45 86
Random interhemispheric point: 120 31 40
Computing 3D gradient x coord...
Computing 3D gradient y coord...
Computing 3D gradient z coord...
Entering Extract3DMaxima
(50 percent threshold: 26) 
Gradient image compression: 1
Determination of the background mean intensity...
Computing 3D gradient x coord...
Computing 3D gradient y coord...
Computing 3D gradient z coord...
edge magnitude minimum: 105
Tissue/background gradient threshold: 105
dist:    0.0
   0.0
   0.4
   0.6
   0.8
   0.9
   0.9
   1.0
   1.1

dist:    0.0
   0.0
   0.4
   0.6
   0.8
   0.9
   0.9
   1.0
   1.1

min_volume=0.000000


------------------------------
!! VIP Error:
	 Negative or NULL limit value!
------------------------------

------------------------------
!! VIP Error:
	 
Execution aborted in function '(distmap)VipComputeFrontPropagationConnectivityDistanceMap'.

------------------------------


------------------------------
!! VIP Error:
	 Negative or NULL limit value!
------------------------------

------------------------------
!! VIP Error:
	 
Execution aborted in function '(distmap)VipComputeFrontPropagationConnectivityDistanceMap'.

------------------------------

Corner background stats: mean: 21.038326; sigma: 48.774193
thbackground=70.312515

merge
Corner background stats: mean: 50.721516; sigma: 65.039719
threshold for corner background/tissue: 116
dist:      1

dist:      1

Background stats: mean: 60.340893; sigma: 53.581482
Global threshold background/tissue: 168
Compute spatial variance...
Deleting last 72 slices
(95 percent threshold: 770) 
8
Compressing volume (forgetting 3 bits)...

Low threshold: 21, High threshold: 100000 (after compression)
             Slice:239
238
237
236
235
234
233
232
231
230
229
228
227
226
225
224
223
222
221
220
219
218
217
216
215
214
213
212
211
210
209
208
207
206
205
204
203
202
201
200
199
198
197
196
195
194
193
192
191
190
189
188
187
186
185
184
183
182
181
180
179
178
177
176
175
174
173
172
171
170
169
168
167
166
165
164
163
162
161
160
159
158
157
156
155
154
153
152
151
150
149
148
147
146
145
144
143
142
141
140
139
138
137
136
135
134
133
132
131
130
129
128
127
126
125
124
123
122
121
120
119
118
117
116
115
114
113
112
111
110
109
108
107
106
105
104
103
102
101
100
 99
 98
 97
 96
 95
 94
 93
 92
 91
 90
 89
 88
 87
 86
 85
 84
 83
 82
 81
 80
 79
 78
 77
 76
 75
 74
 73
 72
 71
 70
 69
 68
 67
 66
 65
 64
 63
 62
 61
 60
 59
 58
 57
 56
 55
 54
 53
 52
 51
 50
 49
 48
 47
 46
 45
 44
 43
 42
 41
 40
 39
 38
 37
 36
 35
 34
 33
 32
 31
 30
 29
 28
 27
 26
 25
 24
 23
 22
 21
 20
 19
 18
 17
 16
 15
 14
 13
 12
 11
 10
  9
  8
  7
  6
  5
  4
  3
  2
  1
  0

strongest high threshold on variance: 36
dist:      1

crest gradient: mean: 8.283361; sigma: 5.007030
threshold gradient: 18
ridge gradient: mean: 8.294411; sigma: 4.077562
threshold gradient: 16
high threshold on variance: 30 (pourcentage: 75)
dist:      1

carto copy full: vs: 0.449997, 0.800003, 0.449997

dist:      1
     2

Max distance: 1.000000 mm
OK
dist:      1

Computing Bias with Kentropy = 1.000000, Kregularization = 20.000000, Kcrest = 20.000000 Koffset = 20.000000
Field sampling: 7x5x7 blocks of 35x19x35 voxels
Number of points for computation: 349732/5358240
Entropy (in the range) before field correction: 5.704782
Range initial average: 48.856662, Initial standard deviation: 13.405333 (349732 points)
With         field   : 49.015697,                           : 13.746180


------------------------------
!! VIP Error:
	 Empty image

------------------------------

------------------------------
!! VIP Error:
	 
Execution aborted in function 'VipComputeBiasFieldMultiGrid'.

------------------------------


Result
Value returned = 111

Expected behavior
With another image and an equivalent command, it works well and generates all expected files correctly:

'VipT1BiasCorrection' '-i' 'baseline_mri_BB336F.nii.gz' '-o' 'VIP_nobias_baseline_mri_BB336F.nii.gz' '-field' 'VIP_biasfield_baseline_mri_BB336F.nii.gz' '-wridge' 'whiteridge_baseline_mri_BB336F.nii.gz' '-ename' 'edges_baseline_mri_BB336F.nii.gz' '-vname' 'variance_baseline_mri_BB336F.nii.gz' '-mname' 'mean_curvature_baseline_mri_BB336F.nii.gz' '-hname' 'hfiltered_baseline_mri_BB336F.nii.gz' '-Dcorrect' 'yes' '-Fwrite' 'yes' '-Wwrite' 'no' '-eWrite' 'no' '-vWrite' 'no' '-mWrite' 'no' '-hWrite' 'no' '-Kentropy' '1.0' '-Kcrest' '20.0' '-Kregul' '20.0' '-Koffset' '20.0' '-sampling' '16.0' '-Grid' '2' '-vp' '75' '-Last' 'auto (AC/PC Points needed)' '-Dkeep' '35.0' '-edges' '3' '-Cweight' 'T2' '-debug' 'no' '-dumb' 'yes' '-Points' 'baseline_mri_BB336F.APC' '-Specie' 'Macaque'

The expected standard output and error:

/casa/host/build/bin/VipT1BiasCorrection 
Command line
'VipT1BiasCorrection' '-i' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/baseline_mri_BB336F.nii.gz' '-o' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/pre_analysis/VIP_nobias_baseline_mri_BB336F.nii.gz' '-field' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/pre_analysis/VIP_biasfield_baseline_mri_BB336F.nii.gz' '-wridge' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/pre_analysis/whiteridge_baseline_mri_BB336F.nii.gz' '-ename' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/pre_analysis/edges_baseline_mri_BB336F.nii.gz' '-vname' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/pre_analysis/variance_baseline_mri_BB336F.nii.gz' '-mname' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/pre_analysis/mean_curvature_baseline_mri_BB336F.nii.gz' '-hname' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/pre_analysis/hfiltered_baseline_mri_BB336F.nii.gz' '-Dcorrect' 'yes' '-Fwrite' 'yes' '-Wwrite' 'no' '-eWrite' 'no' '-vWrite' 'no' '-mWrite' 'no' '-hWrite' 'no' '-Kentropy' '1.0' '-Kcrest' '20.0' '-Kregul' '20.0' '-Koffset' '20.0' '-sampling' '16.0' '-Grid' '2' '-vp' '75' '-Last' 'auto (AC/PC Points needed)' '-Dkeep' '35.0' '-edges' '3' '-Cweight' 'T2' '-debug' 'no' '-dumb' 'yes' '-Points' '/home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/baseline_mri_BB336F.APC' '-Specie' 'Macaque'
Output
3D field regularization
little_opening_size=1.100000

Reading AC, PC, IH coordinates: /home/Petri/BrainVISA/Issues/2022/2022-02-10-Primatologist_biascorrecorrection_issue/data/primatologist_test/subjects/baseline_mri_BB336F/anatomical_mri/default_acquisition/baseline_mri_BB336F.APC
Reading Coordinate file (AC, PC...)
Anterior commissure: 263 29 164
Posterior commissure: 262 40 171
Random interhemispheric point: 263 29 87
Computing 3D gradient x coord...
Computing 3D gradient y coord...
Computing 3D gradient z coord...
Entering Extract3DMaxima
(50 percent threshold: 18) 
Gradient image compression: 1
Determination of the background mean intensity...
Computing 3D gradient x coord...
Computing 3D gradient y coord...
Computing 3D gradient z coord...
edge magnitude minimum: 138
Tissue/background gradient threshold: 138
dist:    0.0
   0.0
   0.2
   0.3
   0.4
   0.5
   0.6
   0.7
   0.8
   0.9
   0.9
   1.0
   1.0
   1.0
   1.0
   1.0
   1.1
   1.1
   1.2
   1.2
   1.2
   1.3
   1.3
   1.3
   1.3
   1.4
   1.4
   1.4
   1.5
   1.5
   1.5
   1.5

dist:    0.0
   0.0
   0.2
   0.3
   0.4
   0.5
   0.6
   0.7
   0.8
   0.9
   0.9
   1.0
   1.0
   1.0
   1.0
   1.0
   1.1
   1.1
   1.2
   1.2
   1.2
   1.3
   1.3
   1.3
   1.3
   1.4
   1.4
   1.4
   1.5
   1.5
   1.5
   1.5

min_volume=0.000000

dist:      1

dist:      1

Corner background stats: mean: 8.367532; sigma: 30.314651
thbackground=39.182182

merge
Corner background stats: mean: 20.117718; sigma: 44.419319
threshold for corner background/tissue: 65
dist:      1

dist:      1

Background stats: mean: 22.568136; sigma: 24.366865
Global threshold background/tissue: 71
Compute spatial variance...
Deleting last 178 slices
(95 percent threshold: 999) 
16
Compressing volume (forgetting 4 bits)...

Low threshold: 4, High threshold: 100000 (after compression)
             Slice:507
506
505
504
503
502
501
500
499
498
497
496
495
494
493
492
491
490
489
488
487
486
485
484
483
482
481
480
479
478
477
476
475
474
473
472
471
470
469
468
467
466
465
464
463
462
461
460
459
458
457
456
455
454
453
452
451
450
449
448
447
446
445
444
443
442
441
440
439
438
437
436
435
434
433
432
431
430
429
428
427
426
425
424
423
422
421
420
419
418
417
416
415
414
413
412
411
410
409
408
407
406
405
404
403
402
401
400
399
398
397
396
395
394
393
392
391
390
389
388
387
386
385
384
383
382
381
380
379
378
377
376
375
374
373
372
371
370
369
368
367
366
365
364
363
362
361
360
359
358
357
356
355
354
353
352
351
350
349
348
347
346
345
344
343
342
341
340
339
338
337
336
335
334
333
332
331
330
329
328
327
326
325
324
323
322
321
320
319
318
290
289
288
287
286
285
284
283
282
281
280
279
278
277
276
275
274
273
272
271
270
269
268
267
266
265
264
263
262
261
260
259
258
257
256
255
254
253
252
251
250
249
248
247
246
245
244
243
242
241
240
239
238
237
236
235
234
233
232
231
230
229
228
227
226
225
224
223
222
221
220
219
218
217
216
215
214
213
212
211
210
209
208
207
206
205
204
203
202
201
200
199
198
197
196
195
194
193
192
191
190
189
188
187
186
185
184
183
182
181
180
179
178
177
176
175
174
173
172
171
170
169
168
167
166
165
164
163
162
161
160
159
158
157
156
155
154
153
152
151
150
149
148
147
146
145
144
143
142
141
140
139
138
137
136
135
134
133
132
131
130
129
128
127
126
125
124
123
122
121
120
119
118
117
116
115
114
113
112
111
110
109
108
107
106
105
104
103
102
101
100
 99
 98
 97
 96
 95
 94
 93
 92
 91
 90
 89
 88
 87
 86
 85
 84
 83
 82
 81
 80
 79
 78
 77
 76
 75
 74
 73
 72
 71
 70
 69
 68
 67
 66
 65
 64
 63
 62
 61
 60
 59
 58
 57
 56
 55
 54
 53
 52
 51
 50
 49
 48
 47
 46
 45
 44
 43
 42
 41
 40
 39
 38
 37
 36
 35
 34
 33
 32
 31
 30
 29
 28
 27
 26
 25
 24
 23
 22
 21
 20
 19
 18
 17
 16
 15
 14
 13
 12
 11
 10
  9
  8
  7
  6
  5
  4
  3
  2
  1
  0

strongest high threshold on variance: 42
dist:      1

crest gradient: mean: 10.912460; sigma: 4.978325
threshold gradient: 21
ridge gradient: mean: 7.707592; sigma: 4.674499
threshold gradient: 17
high threshold on variance: 36 (pourcentage: 75)
dist:      1

carto copy full: vs: 0.225006, 1, 0.225006

dist:      1
     2
     8

Max distance: 7.000000 mm
OK
dist:      1

Computing Bias with Kentropy = 1.000000, Kregularization = 20.000000, Kcrest = 20.000000 Koffset = 20.000000
Field sampling: 8x5x8 blocks of 71x16x71 voxels
Number of points for computation: 3308418/18350080
Entropy (in the range) before field correction: 5.599678
Range initial average: 27.330752, Initial standard deviation: 21.847780 (3308418 points)
With         field   : 27.178062,                           : 21.484234

Range initial average: 37.437164, Initial standard deviation: 6.990573 (238622 points)
With         field   : 37.421499,                           : 7.042779
field increment: about 1.030000
field modif:     -1/   111
    26/   111
    30/   111
    28/   111
    33/   111
    33/   111
    27/   111
    30/   111
    24/   111
    34/   111
    38/   111
    30/   111
    35/   111
    30/   111
    22/   111
    36/   111
    32/   111
    36/   111
    42/   111
    26/   111
    32/   111
    26/   111
    36/   111
    34/   111
    29/   111
    36/   111
    38/   111
    25/   111
    22/   111
    33/   111
    33/   111
    35/   111
    37/   111
    22/   111
    26/   111
    31/   111
    34/   111
    37/   111
    32/   111
    29/   111
    27/   111
    25/   111
    42/   111
    33/   111
    30/   111
    35/   111
    29/   111
    39/   111
    24/   111
    35/   111
    29/   111
    34/   111
    37/   111
    28/   111
    25/   111
    24/   111
    28/   111
    29/   111
    34/   111
    34/   111
    23/   111
    26/   111
    30/   111
    30/   111
    37/   111
    32/   111
    35/   111
    28/   111
    23/   111
    31/   111
    28/   111
    23/   111
    33/   111
    23/   111
    26/   111
    24/   111
    30/   111
    25/   111
    25/   111
    39/   111
    33/   111
    24/   111
    16/   111
    21/   111
    22/   111
    26/   111
    29/   111
    30/   111
    23/   111
    31/   111
    41/   111
    36/   111
    29/   111
    21/   111
    23/   111
    18/   111
    23/   111
    29/   111
    25/   111
    30/   111
    23/   111
    25/   111
    24/   111
    26/   111
    28/   111
    24/   111
    30/   111
    23/   111
    23/   111
    19/   111
    25/   111
    20/   111
    25/   111
    25/   111
    24/   111
    21/   111
    24/   111
    27/   111
    31/   111
    24/   111
    23/   111
    16/   111
    17/   111
    19/   111
    20/   111
    22/   111
    24/   111
    17/   111
    20/   111
    18/   111
    25/   111
    21/   111
    18/   111
    20/   111
    20/   111
    19/   111
     8/   111
    15/   111
    14/   111
    20/   111
    19/   111
    21/   111
    14/   111
    22/   111
    22/   111
    21/   111
    16/   111
    14/   111
    15/   111
    12/   111
    14/   111
    21/   111
    20/   111
    16/   111
    13/   111
    12/   111
    15/   111
    15/   111
    16/   111
    14/   111
    16/   111
    13/   111
    13/   111
     5/   111
     8/   111
     9/   111
    14/   111
    15/   111
    14/   111
    14/   111
    12/   111
    18/   111
     8/   111
     8/   111
    11/   111
     8/   111
     3/   111
     8/   111
    12/   111
     9/   111
     9/   111
     8/   111
     9/   111
     5/   111
     5/   111
    11/   111
     9/   111
     5/   111
     6/   111
     8/   111
     2/   111
     4/   111
     4/   111
     9/   111
    10/   111
     7/   111
     4/   111
     9/   111
     6/   111
     6/   111
     1/   111
     4/   111
     2/   111
     2/   111
     5/   111
     4/   111
     2/   111

Range initial average: 27.330752, Initial standard deviation: 21.847780 (3308418 points)
With         field   : 27.317039,                           : 22.729937

Range initial average: 37.437164, Initial standard deviation: 6.990573 (238622 points)
With         field   : 36.095448,                           : 5.774094

Final entropy: 5.510024
Entropy decrease: 1.627098 percents
Field sampling: 15x9x15 blocks of 35x8x35 voxels
Number of points for computation: 3308418/18350080
Down one level of grid...
carto copy full: vs: 7.87521, 8, 7.87521

Range initial average: 27.330752, Initial standard deviation: 21.847780 (3308418 points)
With         field   : 27.254606,                           : 22.104805

Range initial average: 37.437164, Initial standard deviation: 6.990573 (238622 points)
With         field   : 36.327657,                           : 5.973240
field increment: about 1.020000
field modif:     -1/   697
   166/   697
   156/   697
   139/   697
   119/   697
   107/   697
   112/   697
    98/   697
    79/   697
    77/   697
    62/   697
    70/   697
    62/   697
    56/   697
    53/   697
    41/   697
    44/   697
    42/   697
    41/   697
    45/   697
    38/   697
    38/   697
    36/   697
    38/   697
    32/   697
    29/   697
    24/   697
    30/   697
    30/   697
    30/   697
    26/   697
    23/   697
    25/   697
    24/   697
    24/   697
    24/   697
    19/   697
    20/   697
    17/   697
    17/   697
    16/   697
    17/   697
    25/   697
    24/   697
    15/   697
    22/   697
    23/   697
    20/   697
    21/   697
    22/   697
    16/   697
    22/   697
    16/   697
    25/   697
    22/   697
    16/   697
    16/   697
    15/   697
    16/   697
    22/   697
    16/   697
    15/   697
    15/   697
    25/   697
    14/   697
    17/   697
    11/   697
    16/   697
    16/   697
    22/   697
    15/   697
    12/   697
    14/   697
    18/   697
     8/   697
    11/   697
    14/   697
    11/   697
     7/   697
    13/   697
    14/   697
    12/   697
    13/   697
    13/   697
     8/   697
    16/   697
     7/   697
     7/   697
    11/   697
     9/   697
    10/   697
     8/   697
     6/   697

field increment: about 1.010000
field modif:     78/   697
    60/   697
    55/   697
    41/   697
    36/   697
    34/   697
    31/   697
    31/   697
    35/   697
    29/   697
    27/   697
    26/   697
    25/   697
    21/   697
    20/   697
    30/   697
    20/   697
    29/   697
    17/   697
    22/   697
    12/   697
    10/   697
    15/   697
    17/   697
    10/   697
    12/   697
    15/   697
     7/   697
    20/   697
    14/   697
    16/   697
    14/   697
    15/   697
    11/   697
    14/   697
    14/   697
     9/   697
    13/   697
    10/   697
     9/   697
     9/   697
     6/   697

Range initial average: 27.330752, Initial standard deviation: 21.847780 (3308418 points)
With         field   : 27.320780,                           : 24.946840

Range initial average: 37.437164, Initial standard deviation: 6.990573 (238622 points)
With         field   : 34.220393,                           : 4.887557

Final entropy: 5.472097
Entropy decrease: 2.331467 percents
Resampling field using cubic spline
Correcting volume...
Slice:  1
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512


Result
Value returned = 0

Screenshots
Not applicable

Environment:

  • Engine: Singularity
  • Version of BrainVISA: 5.0 branch
  • For local builds, version of the casa-dev image casa-dev-5.0-8

Additional context
Not applicable
@nsouedet nsouedet added the bug Something isn't working label Feb 10, 2022
@nsouedet nsouedet self-assigned this Feb 10, 2022
@nsouedet
Copy link
Contributor Author

Ok, the issue is due to an implicit conversion from float to int in function VipConnectivityChamferErosion function, but the estimated chamfer size (based on volume voxel size) is less than one for BB339F image. So it is rounded to 0, which is not suitable for chamfer erosion size.

@nsouedet
Copy link
Contributor Author

nsouedet commented Feb 11, 2022 •
edited
Loading

In fact, Check2DMorphoSizeConsistence returns ok for sizes over 0, but I think that VIP morpho functions that uses VipComputeFrontPropagationConnectivityDistanceMap all fails for sizes in [0, 1]

@nsouedet
Copy link
Contributor Author

nsouedet commented Feb 11, 2022 •
edited
Loading

Another issue follows the first one. White ridges are not properly detected on BB339F data that makes fail the bias correction.
This is because initiale gradient image used to process ridges is not correct

@nsouedet
Copy link
Contributor Author

nsouedet commented Feb 14, 2022 •
edited
Loading

The reason is that not enough white matter is kept and the main connected component kept is one of the muscles.

@nsouedet
Copy link
Contributor Author

A temporary simple solution may be to manually crop the data to remove the main muscle part

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@nsouedet nsouedet

Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@nsouedet