Dear SPM experts,
We have been trying to segment some T1 data from OASIS 3 on a Linux (Ubuntu) 32 core machine. Everything went normally in the beginning, but one after one the jobs bailed out with the following error message. Apparently the data were identified as non-T1, and then some other problems ocurred. Even though the default error handling (skip and process next) was chosen processing halted after a while completely.
Any help is appreciated, thaks a lot!
Chris
AT12.8.1 r1987: 1/1: ./sub-OAS30038_ses-d1214_run-03_T1w.nii
------------------------------------------------------------------------
SANLM denoising (medium): 15s
APP: Rough bias correction:
Initialize 3s
Estimate background 1s
Initial correction 5s
Refine background 2s
Final correction 3s
Final scaling 4s
21s
Correct center-of-mass 21s
Affine registration 16s
SPM preprocessing 1 (estimate 1 - TPM registration): 13s
Use initial fine affine registration. 23s
SPM preprocessing 1 (estimate 2): 62s
----------------------------------------------------------------------------
WARNING 01: cat_run_job1639:nonT1contrast
A non-T1 contrast was detected and the NEW EXPERIMENTAL
PIPELINE is used! If it is was a high-resolution T1 image,
the initial segmentation might have failed, probably due
to alignment problems (please check the image orientation).
----------------------------------------------------------------------------
SPM preprocessing 2 (write):
Write Segmentation 8s
Update segmentation 6s
Update skull-stripping 5s
Update probability maps 3s
Update registration 21s
43s
Global intensity correction: SANLM denoising after intensity normalization (medium): 2s
------------------------------------------------------------------------
NOTE 01: cat_main:skipLAS
Skip LAS due to image contrast. Use global normalization.
------------------------------------------------------------------------
13s
SANLM denoising after LAS (medium) 18s
20s
--- Update Ym and Ymi ---
ROI segmentation (partitioning):
Atlas -> subject space 2s
Major structures 1s
Ventricle detection 5s
Blood vessel detection 1s
Manual stroke lesion detection 0s
Closing of deep structures 0s
Side alignment 1s
Final corrections 1s
11s
Amap using initial SPM12 segmentations (MRF filter strength 0.07): 30s
AMAP peaks: [0.67±0.07,0.47±0.11,1.00±0.04]
--- Update Ym and Ymi ---
Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
Template: "/home/weisech/Schreibtisch/Imaging/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"
1 | 2.50 | 0.1897 0.0000 0.1897 | 32.0000
2 | 2.50 | 0.1772 0.0040 0.1812 | 29.4886
3 | 2.50 | 0.1727 0.0068 0.1795 | 26.9772
4 | 2.50 | 0.1702 0.0083 0.1785 | 24.6107
5 | 2.50 | 0.1682 0.0093 0.1775 | 22.6548
6 | 2.50 | 0.1665 0.0101 0.1765 | 20.6989
7 | 2.50 | 0.1645 0.0108 0.1753 | 18.9688
8 | 2.50 | 0.1626 0.0117 0.1742 | 17.4455
9 | 2.50 | 0.1606 0.0123 0.1730 | 15.9223
10 | 2.50 | 0.1585 0.0133 0.1717 | 14.6627
11 | 2.50 | 0.1563 0.0141 0.1704 | 13.4764
12 | 2.50 | 0.1541 0.0148 0.1689 | 12.3015
13 | 2.50 | 0.1516 0.0159 0.1675 | 11.3776
14 | 2.50 | 0.1493 0.0167 0.1659 | 10.4537
15 | 2.25 | 0.1844 0.0177 0.2021 | 9.5920
16 | 2.25 | 0.1723 0.0247 0.1971 | 8.8725
17 | 2.25 | 0.1657 0.0281 0.1937 | 8.1530
18 | 2.25 | 0.1604 0.0303 0.1906 | 7.5234
19 | 2.25 | 0.1556 0.0320 0.1876 | 6.9630
20 | 2.25 | 0.1512 0.0332 0.1844 | 6.4027
21 | 2.25 | 0.1467 0.0347 0.1814 | 5.9447
22 | 2.25 | 0.1425 0.0358 0.1782 | 5.5083
23 | 2.25 | 0.1383 0.0366 0.1749 | 5.0803
24 | 2.25 | 0.1335 0.0378 0.1713 | 4.7404
25 | 2.25 | 0.1296 0.0385 0.1680 | 4.4005
26 | 2.25 | 0.1256 0.0391 0.1648 | 4.0868
27 | 2.25 | 0.1218 0.0400 0.1617 | 3.8221
28 | 2.25 | 0.1181 0.0404 0.1585 | 3.5574
29 | 2.00 | 0.1169 0.0406 0.1575 | 3.3283
30 | 2.00 | 0.1119 0.0414 0.1533 | 3.1221
31 | 2.00 | 0.1086 0.0414 0.1500 | 2.9160
32 | 2.00 | 0.1050 0.0417 0.1467 | 2.7495
33 | 2.00 | 0.1022 0.0417 0.1439 | 2.5890
34 | 2.00 | 0.0995 0.0416 0.1411 | 2.4330
35 | 2.00 | 0.0968 0.0418 0.1387 | 2.3080
36 | 2.00 | 0.0944 0.0418 0.1361 | 2.1830
37 | 2.00 | 0.0919 0.0417 0.1337 | 2.0688
38 | 2.00 | 0.0896 0.0418 0.1315 | 1.9714
39 | 2.00 | 0.0875 0.0417 0.1292 | 1.8740
40 | 2.00 | 0.0850 0.0417 0.1267 | 1.7907
41 | 2.00 | 0.0832 0.0416 0.1248 | 1.7148
42 | 2.00 | 0.0814 0.0414 0.1228 | 1.6390
43 | 1.75 | 0.0797 0.0408 0.1205 | 1.5785
44 | 1.75 | 0.0769 0.0416 0.1185 | 1.5194
45 | 1.75 | 0.0751 0.0417 0.1168 | 1.4626
46 | 1.75 | 0.0736 0.0418 0.1154 | 1.4166
57 | 1.50 | 0.0750 0.0332 0.1082 | 1.0900
Problem with Shooting (dets: 0.00271124 .. 5.17685)
58 | 1.50 | 0.0674 0.0385 0.1059 | 1.0730
59 | 1.50 | 0.0641 0.0406 0.1047 | 1.0579
Shooting registration with 2.50:-0.25:1.50 mm takes: 144s
Prepare output 5s
149s
Jacobian determinant (RMS): 0.025 0.126 0.334 0.606 1.453 | 0.978213
Template Matching: 0.190 0.184 0.117 0.221 0.192 | 0.192248
Write result maps: 4s
Surface and thickness estimation:
lh:
Thickness estimation (0.50 mm³):
WM distance: 10s
CSF distance: 5s
PBT2x thickness: 17s
34s
Create initial surface 22s
Topology correction: 895s
Surface refinement: 146s
Reduction of surface collisions with optimization: 179s
Spherical mapping with areal smoothing 85s
Spherical registration 201s
rh:
Thickness estimation (0.50 mm³):
WM distance: 11s
CSF distance: 5s
PBT2x thickness: 16s
34s
Create initial surface 21s
Topology correction: 24s
Surface refinement: 27s
Reduction of surface collisions with optimization: 33s
Spherical mapping with areal smoothing 24s
Spherical registration 217s
Final surface processing results:
Average thickness (FS): 1.3893 ± 0.9904 mm
Surface intensity / position RMSE: 0.1692 / 0.5044
Euler number / defect number / defect size: 20.0 / 8.5 / 48.26%
Display thickness: /home/weisech/Schreibtisch/BadImages/surf/lh.thickness.sub-OAS30038_ses-d1214_run-03_T1w
Display thickness: /home/weisech/Schreibtisch/BadImages/surf/rh.thickness.sub-OAS30038_ses-d1214_run-03_T1w
Show surfaces in orthview: /home/weisech/Schreibtisch/BadImages/sub-OAS30038_ses-d1214_run-03_T1w.nii
Surface ROI estimation: 2227s
Surface and thickness estimation takes: 2193s
ROI estimation in native space:
ROI estimation of 'cobra' atlas 2s
ROI estimation of 'neuromorphometrics' atlas 6s
Write results 6s
8s
Quality check:
------------------------------------------------------------------------
CAT Preprocessing error for sub-OAS30038_ses-d1214_run-03_T1w:
------------------------------------------------------------------------
Unrecognized function or variable 'red'.
------------------------------------------------------------------------
1069 - cat_vol_qa
918 - cat_main
1265 - cat_run_job1639
40 - cat_run_newcatch
1108 - run_job
647 - cat_run
29 - cfg_run_cm
1717 - local_runcj
972 - cfg_util
710 - MenuFileRun_Callback
95 - gui_mainfcn
53 - cfg_ui
------------------------------------------------------------------------
25-May-2022 14:39:18 - Failed 'CAT12: Segmentation'
Unrecognized function or variable 'Pp0'.
In file "/home/weisech/Schreibtisch/Imaging/spm12/toolbox/cat12/cat_vol_qa.m" (v1982), function "cat_vol_qa" at line 1091.
In file "/home/weisech/Schreibtisch/Imaging/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 204.
In file "/home/weisech/Schreibtisch/Imaging/spm12/toolbox/cat12/cat_run.m" (v1984), function "run_job" at line 1108.
In file "/home/weisech/Schreibtisch/Imaging/spm12/toolbox/cat12/cat_run.m" (v1984), function "cat_run" at line 647.
The following modules did not run:
Failed: CAT12: Segmentation
|