Dear Amir,
looks like some SPM12 windows were closed during preprocessing.
Best,
Christian
On Tue, 25 Dec 2018 03:16:32 +0000, Amirhossein Modabbernia <[log in to unmask]> wrote:
>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
>
>
>
>------------------------------------------------------------------------
>CAT12.5 r1364: 2/12: ./BL_analyzing/1617607.nii
>------------------------------------------------------------------------
>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
>
>------------------------------------------------------------------------
>CAT Preprocessing error for 1617607:
>------------------------------------------------------------------------
>Invalid or deleted object.
>------------------------------------------------------------------------
> 312 - spm_figure
> 2281 - cat_main
> 721 - cat_run_job1070
> 16 - cat_run_newcatch
> 398 - run_job
> 161 - cat_run
>------------------------------------------------------------------------
> 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);
>}
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