Dear Christopher,
image orientation of that OASIS subject is wrong and therefore automatic estimation of T1-contrast fails.
Best,
Christian
On Fri, 27 May 2022 12:00:59 +0100, Chris Weise <[log in to unmask]> wrote:
>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
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