Hi All,
While running preprocessing steps for structural data in CAT12 with multiple processes, I get the following error for some of the processes (see the last part of the report below). Could anyone please tell me what the problem is? what does "Invalid or deleted object." refer to and how can one fix the problem?
Regards,
Amir
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CAT12.5 r1364: 2/12: ./BL_analyzing/1617607.nii
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SANLM denoising (medium): 120s
APP: Rough bias correction:
Initialize 11s
Estimate background 58s
Initial correction 16s
Refine background 35s
Final correction 13s
Background correction 1s
Final scaling 5s
139s
Coarse affine registration 19s
Affine registration 36s
SPM preprocessing 1 (estimate 1): 27s
SPM preprocessing 1 (estimate 2): 631s
SPM preprocessing 1 (estimate skull-stripped): 247s
SPM preprocessing 1 (estimate skull-stripped): 267s
SPM preprocessing 2 (write):
Write Segmentation 40s
Update Segmentation 99s
Update Skull-Stripping 13s
Update probability maps 15s
167s
Global intensity correction: 33s
SANLM denoising after intensity normalization (medium): 21s
Fast Shooting registration 112s
Local adaptive segmentation (LASstr=0.50):
Prepare maps 10s
Prepare partitions 3s
Prepare segments (LASmod = 1.00) 32s
Estimate local tissue thresholds (WM) 57s
Estimate local tissue thresholds (GM) 58s
Estimate local tissue thresholds (CSF/BG) 9s
Intensity transformation 176s
SANLM denoising after LAS (medium) 28s
28s
ROI segmentation (partitioning):
Atlas -> subject space 14s
Major structures 7s
Ventricle detection 27s
Blood vessel detection 19s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 62s
Manual stroke lesion detection 0s
Closing of deep structures 3s
Side alignment 8s
Final corrections 8s
147s
Blood vessel correction (BVCstr=0.50): 3s
Amap using initial SPM12 segmentations (MRF filter strength 0.07): 42s
AMAP peaks: [CSF,GM,WM] = [0.46±0.06,0.68±0.09,0.98±0.04]
Final cleanup (gcutstr=0.23):
Level 1 cleanup (ROI estimation) 9s
Level 1 cleanup (brain masking) 4s
Level 2 cleanup (CSF correction) 2s
Level 3 cleanup (CSF/WM PVE) 4s
19s
Dartel registration with 1.50 mm on a 1.50 mm Template:
Template: "/Users/amirhosseinmodabbernia/spm12/toolbox/cat12/templates_1.50mm/Template_1_IXI555_MNI152.nii"
1 | 0.1512 | 481394 0 481394 0.000
2 | 0.1205 | 383729 29781 413511 0.000
3 | 0.1190 | 379066 28112 407178 0.000
4 | 0.1195 | 380491 14639 395130 0.000
5 | 0.1100 | 350319 34482 384801 0.000
6 | 0.1101 | 350601 33173 383774 0.000
7 | 0.1112 | 353980 17324 371304 0.000
8 | 0.1017 | 323946 36661 360607 0.000
9 | 0.1016 | 323459 35849 359308 0.000
10 | 0.1026 | 326762 18839 345601 0.000
11 | 0.0928 | 295374 38626 334001 0.000
12 | 0.0922 | 293639 38645 332284 0.000
13 | 0.0931 | 296568 20381 316949 0.000
14 | 0.0841 | 267929 37557 305486 0.000
15 | 0.0831 | 264583 38891 303474 0.000
16 | 0.0827 | 263280 40889 304169 0.000
17 | 0.0823 | 261929 41187 303116 0.000
18 | 0.0819 | 260681 42102 302783 0.000
548s
Jacobian determinant (RMS): 0.130818
Template Matching: 0.081862
Write result maps: 35s
Surface and thickness estimation:
lh:
Thickness estimation (0.50 mm³):
WM distance: 127s
CSF distance: 98s
PBT2x thickness: 57s
305s
313s
Create initial surface 87s
Topology correction and surface refinement: 119s
Refine central surface 162s
Correction of central surface in highly folded areas 2 7s
Spherical mapping with areal smoothing 266s
Spherical registration 592s
Surface Euler number: -2
Overall size of topology defects: 59
rh:
Thickness estimation (0.50 mm³):
WM distance: 131s
CSF distance: 95s
PBT2x thickness: 65s
320s
332s
Create initial surface 118s
Topology correction and surface refinement: 122s
Refine central surface 155s
Correction of central surface in highly folded areas 2 7s
Spherical mapping with areal smoothing 259s
Spherical registration 578s
Surface Euler number: -2
Overall size of topology defects: 131
Display thickness: /Volumes/Seagate Backup Plus Drive/BL_analyzing/surf/lh.thickness.1617607
Display thickness: /Volumes/Seagate Backup Plus Drive/BL_analyzing/surf/rh.thickness.1617607
Surface and thickness estimation: 3166s
ROI estimation:
Data mapping to normalized atlas space 533s
ROI estimation of 'cobra' atlas 222s
Data mapping to normalized atlas space 627s
ROI estimation of 'neuromorphometrics' atlas 22s
ROI estimation of 'lpba40' atlas 14s
1418s
Quality check: 14s
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CAT Preprocessing error for 1617607:
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Invalid or deleted object.
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312 - spm_figure
2281 - cat_main
721 - cat_run_job1070
16 - cat_run_newcatch
398 - run_job
161 - cat_run
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Warning:cat_io_report:CATgui: Incomplete report creation in cat_io_report because of incomplete CAT parameters.
Developer display mode!
Print 'Graphics' figure to:
/Volumes/Seagate Backup Plus Drive/BL_analyzing/report/catreport_1617607.pdf
{Error using matlab.ui.Figure/set
Invalid or deleted object.
Error in spm_figure (line 312)
if ~isdocked, set(F,'Position',pos); end
Error in cat_main (line 2281)
spm_figure('Clear','Graphics');
Error in cat_run_job1070 (line 721)
cat_main(res,obj.tpm,job);
Error in cat_run_newcatch (line 16)
cat_run_job1070(job,tpm,subj);
Error in cat_run>run_job (line 398)
cat_run_newcatch(job,tpm,subj);
Error in cat_run (line 161)
varargout{1} = run_job(job);
}
