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SPM  January 2019

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Subject:

Re: CAT Preprocessing Error

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Wed, 2 Jan 2019 10:15:33 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (184 lines)

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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