Dear Christian and other CAT12 users,
I’m using the latest version of CAT12.8 (r1844) in Matlab 2018b, SPM12(v7771).
I receive the attached error right at the end of my segmentation step; see attached log.
I’m not sure I understand why, as I processed an independent cohort without any issue.
Do you have any idea?
Thanks in advance.
Yann
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September 15, 2014
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CAT parallel processing with MATLAB PID: 5235
------------------------------------------------------------------------
CAT12.8-Beta r1844: 1/133: ./Subjects/100109/100109.nii
------------------------------------------------------------------------
SANLM denoising (medium): 54s
APP: Rough bias correction:
Initialize 14s
Estimate background 13s
Initial correction 18s
Refine background 7s
Final correction 13s
Final scaling 12s
88s
Correct center-of-mass 11s
Affine registration 45s
SPM preprocessing 1 (estimate 1 - TPM registration): 198s
SPM preprocessing 1 (estimate 2): 228s
SPM preprocessing 2 (write):
Write Segmentation 31s
Update Segmentation 35s
Update Skull-Stripping 82s
Update probability maps 10s
158s
Global intensity correction: 34s
SANLM denoising after intensity normalization (medium): 14s
Fast Optimized Shooting registration 61s
Local adaptive segmentation (LASstr=0.50):
Prepare maps 13s
Prepare partitions 3s
Prepare segments (LASmod = 1.05) 32s
Estimate local tissue thresholds (WM) 30s
Estimate local tissue thresholds (GM) 35s
Estimate local tissue thresholds (CSF/BG) 8s
Intensity transformation
0s
SANLM denoising after LAS (medium) 27s
153s
ROI segmentation (partitioning):
Atlas -> subject space 20s
Major structures 12s
Ventricle detection 30s
Blood vessel detection 18s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 69s
Manual stroke lesion detection 0s
Closing of deep structures 4s
Side alignment 10s
Final corrections 5s
168s
Blood vessel correction (BVCstr=0.50): 2s
Amap using initial SPM12 segmentations (MRF filter strength 0.05): 100s
AMAP peaks: [CSF,GM,WM] = [0.36±0.06,0.68±0.07,0.98±0.05]
Final cleanup (gcutstr=0.25):
Level 1 cleanup (ROI estimation) 12s
Level 1 cleanup (brain masking) 6s
Level 2 cleanup (CSF correction) 3s
Level 3 cleanup (CSF/WM PVE) 6s
26s
Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
Template: "/mridata/workingdata/RUSE/spm12_cat12.8/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"
1 | 2.50 | 0.0834 0.0000 0.0834 | 32.0000
2 | 2.50 | 0.0813 0.0011 0.0824 | 29.4886
3 | 2.50 | 0.0808 0.0016 0.0823 | 26.9772
4 | 2.50 | 0.0805 0.0017 0.0822 | 24.6107
5 | 2.50 | 0.0802 0.0018 0.0821 | 22.6548
6 | 2.50 | 0.0800 0.0019 0.0819 | 20.6989
7 | 2.50 | 0.0798 0.0019 0.0818 | 18.9688
8 | 2.50 | 0.0796 0.0020 0.0816 | 17.4455
9 | 2.50 | 0.0794 0.0021 0.0814 | 15.9223
10 | 2.50 | 0.0791 0.0021 0.0812 | 14.6627
11 | 2.50 | 0.0789 0.0022 0.0811 | 13.4764
12 | 2.50 | 0.0786 0.0022 0.0808 | 12.3015
13 | 2.50 | 0.0784 0.0023 0.0807 | 11.3776
14 | 2.50 | 0.0781 0.0023 0.0805 | 10.4537
15 | 2.25 | 0.0768 0.0024 0.0791 | 9.5920
16 | 2.25 | 0.0741 0.0037 0.0778 | 8.8725
29 | 2.00 | 0.0757 0.0016 0.0774 | 3.3283
30 | 2.00 | 0.0697 0.0040 0.0738 | 3.1221
31 | 2.00 | 0.0678 0.0050 0.0728 | 2.9160
43 | 1.75 | 0.0671 0.0028 0.0699 | 1.5785
44 | 1.75 | 0.0626 0.0052 0.0678 | 1.5194
45 | 1.75 | 0.0612 0.0060 0.0672 | 1.4626
57 | 1.50 | 0.0596 0.0043 0.0639 | 1.0900
58 | 1.50 | 0.0564 0.0064 0.0628 | 1.0730
59 | 1.50 | 0.0553 0.0071 0.0624 | 1.0579
Shooting registration with 2.50:-0.25:1.50 mm takes: 258s
Prepare output 20s
278s
Jacobian determinant (RMS): 0.101381
Template Matching: 0.166032
Write result maps: 14s
Surface and thickness estimation:
lh:
Thickness estimation (0.50 mm³):
WM distance: 133s
CSF distance: 45s
PBT2x thickness: 149s
346s
Create initial surface 160s
Topology correction: 270s
Surface refinement: 209s
Reduction of surface collisions with optimization: 172s
Spherical mapping with areal smoothing 204s
Spherical registration 334s
rh:
Thickness estimation (0.50 mm³):
WM distance: 139s
CSF distance: 45s
PBT2x thickness: 145s
346s
Create initial surface 156s
Topology correction: 286s
Surface refinement: 166s
Reduction of surface collisions with optimization: 199s
Spherical mapping with areal smoothing 208s
Spherical registration 307s
Final surface processing results:
Average thickness: 2.6964 ± 0.7728 mm
Euler characteristic / defect size: 20 / 0.28%
Display thickness: /mridata/workingdata/Subjects/100109/surf/lh.thickness.100109
Display thickness: /mridata/workingdata/Subjects/100109/surf/rh.thickness.100109
Show surfaces in orthview: /mridata/workingdata/Subjects/100109/100109.nii
Surface ROI estimation: Surface and thickness estimation takes: 3529s
ROI estimation:
ROI estimation of 'cobra' atlas 11s
ROI estimation of 'neuromorphometrics' atlas 39s
ROI estimation of 'lpba40' atlas 11s
ROI estimation of 'hammers' atlas 28s
ROI estimation of 'thalamus' atlas 2s
ROI estimation of 'ibsr' atlas 10s
Write results 10s
102s
Quality check: 8s
------------------------------------------------------------------------
CAT Preprocessing error for 100109:
------------------------------------------------------------------------
Vectors must be the same length.
------------------------------------------------------------------------
1011 - cat_main_reportfig
967 - cat_main1639
1086 - cat_run_job1639
40 - cat_run_newcatch
919 - run_job
501 - cat_run
------------------------------------------------------------------------
{Reference to a cleared variable cat_err_res.
Error in cat_run_newcatch (line 201)
if isfield(cat_err_res,'res')
Error in cat_run>run_job (line 919)
cat_run_newcatch(job,tpm,subj);
Error in cat_run (line 501)
varargout{1} = run_job(job);
}
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