Dear Andreia,
please can you try to change line 421 in cat_surf_createCS.m to:
cmd = sprintf('CAT_FixTopology -lim 128 -bw 512 -n 81920 -refine_length 2 "%s" "%s" "%s"',Praw,Psphere0,Pcentral);
Maybe, the new laplace option causes these problems.
Best,
Christian
On Thu, 29 Jun 2017 15:37:21 +0100, Andreia N. Queirós <[log in to unmask]> wrote:
>[Please ignore the previous post due to error in formating]
>
>Dear CAT experts,
>
>this is the first time that our research group is resorting to the CAT12 toolbox.
>We need to obtain volume and surface measures for structures such as the left and right insula.
>
>In the preprocessing stage, when we are running the segment data analysis, Cat12 is able to generate GM, WM, and CSF. however, most of the time (about 9 in every 10 trials), it crashes before surface generation. Please see the error message below, copied from the Matlab command window.
>
>Error message starts here (Please find attached the complete at the end of this post):
>a pop up message box appears with the following text: "CAT_FixTopology.exe has stopped working" prior to the following log:
>------------------------------------------------------------------------
>CAT Preprocessing error: CAT:system_error: . 27 - cat_check_system_output
>423 - cat_surf_createCS
>1637 - cat_main
>634 - cat_run_job1070
>14 - cat_run_newcatch
>276 - run_job
>155 - cat_run
>29 - cfg_run_cm
>1688 - local_runcj
>959 - cfg_util
>703 - MenuFileRun_Callback
>95 - gui_mainfcn
>53 - cfg_ui
>------------------------------------------------------------------------
>Error:cat_io_report:CATgui: Error in cat_io_report GUI parameter report creation > incomple CAT parameters.
>
>
>What we find very odd is that the exact same analysis (i.e., same .nii files with the same parameters) most of the time fails, however, at times it runs until its completion.
>
>Our hardware/software settings are as follows:
>* System: Windows 10 Home - 1607 / 64-bit
>* Matlab: R2015a
>* SPM12 (v6906)
>* CAT12 (r1148)
>
>We've already tried the following solutions as per recommendations in previous posts:
>* Set the number os processes to "0"
>* Substituted the file "cat_check_system_output.m" in the Cat12 folder
>* Tested that we are able to display gifti files using the "spm_mesh_render" function
>* Tested the previous versions of CAT12: r1147 and the r1113
>* Tested another Windows version: Windows 10 Pro - 1703 / 64-bit
>Please note that we always run Cat12 without any other software running simultaneously.
>
>We thank you in advance for any help you can give us. We are at a loss as what to do next.
>
>Best regards,
>Andreia N. Queirós
>
>
>
>
>
>
>««««««««««««««««««««««««««««««««««««»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»
>
> ___ ____ __ __
>/ __)( _ \( \/ )
>\__ \ )___/ ) ( Statistical Parametric Mapping
>(___/(__) (_/\/\_) SPM12 - http://www.fil.ion.ucl.ac.uk/spm/
>
>
>SPM12: v6906 14:47:38 - 29/06/2017
>========================================================================
>Initialising SPM : ........done
>
>SPM present working directory:
> C:\Program Files\MATLAB\MATLAB Production Server\R2015a\bin
>>> cat12
>
>SPM12: spm_cat12 (vCAT12) 14:48:01 - 29/06/2017
>========================================================================
>
> _______ ___ _______
> | ____/ / _ \ \_ _/
> | |___ / /_\ \ | | Computational Anatomy Toolbox
> |____/ /_/ \_\ |_| CAT12 - http://www.neuro.uni-jena.de
>
> CAT default file:
> C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_defaults.m
>
>
>
>------------------------------------------------------------------------
>Running job #1
>------------------------------------------------------------------------
>Running 'CAT12: Segmentation'
>
>------------------------------------------------------------------------
>CAT12 r1148: 1/1: .\nifti\sB003023-0016-00001-000176-01.nii
>------------------------------------------------------------------------
>APP: Rough bias correction:
> Initialize 6s
> Estimate background 3s
> Initial correction 8s
> Refine background 5s
> Final correction 6s
> Background correction 1s
> Final scaling 4s
> 33s
>Coarse affine registration 24s
>Affine registration 9s
>SPM preprocessing 1 (estimate): 106s
>SPM preprocessing 2 (write): 102s
>Global intensity correction: 21s
>SANLM noise correction: 20s
>Local adaptive segmentation (LASstr=0.50):
> Prepare maps 5s
> Prepare partitions 3s
> Prepare segments (LASmod = 1.04) 24s
> Estimate local tissue thresholds 68s
> SANLM noise correction for LAS 18s
> 118s
>ROI segmentation (partitioning):
> Atlas -> subject space 10s
> Major structures 8s
> Ventricle detection 13s
> Blood vessel detection 6s
> WMH detection (WMHCstr=0.50) 20s
> Closing of deep structures 3s
> Side alignment 8s
> Final corrections 4s
> 72s
>Blood vessel correction (BVCstr=0.50): 3s
>Skull-stripping using graph-cut (gcutstr=0.50):
> WM initialisation 7s
> GM region growing 2s
> GM-CSF region growing 7s
> CSF region growing 8s
> Ventricle filling 5s
> 29s
>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 42s
> AMAP peaks: [CSF,GM,WM] = [0.41±0.07,0.68±0.08,0.98±0.04]
>Final cleanup (gcutstr=0.50):
> Level 1 cleanup (ROI estimation) 6s
> Level 1 cleanup (brain masking) 3s
> Level 2 cleanup (CSF correction) 3s
> Level 3 cleanup (CSF/WM PVE) 2s
> 14s
>Internal WMH correction for spatial normalization (WMHCstr=0.50): 5s
>Dartel registration with 1.50 mm:
> 1 | 0.2105 | 446828 0 446828 364.853
> 2 | 0.1744 | 370176 22592 392768 177.532
> 3 | 0.1703 | 361552 22796 384348 59.553
> 4 | 0.1700 | 360991 12113 373104 180.362
> 5 | 0.1571 | 333483 29955 363438 64.433
> 6 | 0.1571 | 333437 29200 362637 37.751
> 7 | 0.1583 | 336097 15161 351258 154.942
> 8 | 0.1450 | 307887 33370 341257 56.192
> 9 | 0.1448 | 307480 32790 340270 32.778
> 10 | 0.1461 | 310233 17136 327369 139.878
> 11 | 0.1322 | 280555 35906 316460 54.727
> 12 | 0.1315 | 279153 35805 314959 34.261
> 13 | 0.1327 | 281689 18915 300603 116.736
> 14 | 0.1201 | 254984 35110 290094 50.467
> 15 | 0.1188 | 252100 36182 288282 32.212
> 16 | 0.1183 | 251169 38053 289222 38.995
> 17 | 0.1177 | 249788 38462 288250 27.517
> 18 | 0.1171 | 248683 39277 287960 24.543
> 272s
>Write result maps: 35s
>Surface and thickness estimation:
>lh:
> Thickness estimation (0.50 mm³):
> WM distance: 61s
> CSF distance: 56s
> PBT2x thickness: 37s
> Final Corrections: 169s
> Create initial surface
>Setting up...
>Starting main process...
>Done with 10 percent.
>Done with 20 percent.
>Done with 30 percent.
>Done with 40 percent.
>Done with 50 percent.
>Done with 60 percent.
>Done with 70 percent.
>Done with 80 percent.
>Done with 90 percent.
>Done with 100 percent.
>Made 42 adjustments.
>Extracting component with largest number of vertices...
>Vertices: 601414 Triangles: 1202840
>Setting up...
>Starting main process...
>Done with 10 percent.
>Done with 20 percent.
>Done with 30 percent.
>Done with 40 percent.
>Done with 50 percent.
>Done with 60 percent.
>Done with 70 percent.
>Done with 80 percent.
>Done with 90 percent.
>Done with 100 percent.
>Made 30 adjustments.
>Extracting component with largest number of vertices...
>Vertices: 601536 Triangles: 1203084
> 18s
> Reduce surface to 100000 faces: Resampled into 251284 polygons.
>Extract largest of 120 components.
> 37s
> Topology correction and surface refinement
>------------------------------------------------------------------------
>CAT Preprocessing error: CAT:system_error: . 27 - cat_check_system_output
> 423 - cat_surf_createCS
> 1637 - cat_main
> 634 - cat_run_job1070
> 14 - cat_run_newcatch
> 276 - run_job
> 155 - cat_run
> 29 - cfg_run_cm
> 1688 - local_runcj
> 959 - cfg_util
> 703 - MenuFileRun_Callback
> 95 - gui_mainfcn
> 53 - cfg_ui
>------------------------------------------------------------------------
> Error:cat_io_report:CATgui: Error in cat_io_report GUI parameter report creation > incomple CAT parameters.
>Warning: Error updating Text.
>
> String must have valid interpreter syntax:
>..cuments\Software\_fMRI\spm12\tpm\TPM.nii
>
>> In defaulterrorcallback (line 12)
> In spm_orthviews>redraw (line 1459)
> In spm_orthviews>redraw_all (line 1466)
> In spm_orthviews (line 280)
> In cat_io_report (line 392)
> In cat_run_newcatch (line 67)
> In cat_run>run_job (line 276)
> In cat_run (line 155)
> In cfg_run_cm (line 29)
> In cfg_util>local_runcj (line 1688)
> In cfg_util (line 959)
> In cfg_ui>MenuFileRun_Callback (line 703)
> In gui_mainfcn (line 95)
> In cfg_ui (line 53)
>Warning: Error updating Text.
>
> String must have valid interpreter syntax:
>..tes\_1.50mm\Template\_1\_IXI555\_MNI152.nii
>
>> In defaulterrorcallback (line 12)
> In spm_orthviews>redraw (line 1459)
> In spm_orthviews>redraw_all (line 1466)
> In spm_orthviews (line 280)
> In cat_io_report (line 392)
> In cat_run_newcatch (line 67)
> In cat_run>run_job (line 276)
> In cat_run (line 155)
> In cfg_run_cm (line 29)
> In cfg_util>local_runcj (line 1688)
> In cfg_util (line 959)
> In cfg_ui>MenuFileRun_Callback (line 703)
> In gui_mainfcn (line 95)
> In cfg_ui (line 53)
>
>Print 'Graphics' figure to:
> C:\Users\andre\Desktop\Participante4\nifti\report\catreport_sB003023-0016-00001-000176-01.pdf
>Failed 'CAT12: Segmentation'
>Error using cat_check_system_output (line 27)
>'find_selfintersections: .......................................................'
>In file "C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_check_system_output.m" (v1022), function "cat_check_system_output" at line 27.
>In file "C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_surf_createCS.m" (v1137), function "cat_surf_createCS" at line 423.
>In file "C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_main.m" (v1145), function "cat_main" at line 1637.
>In file "C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_run_job1070.m" (v1147), function "cat_run_job1070" at line 634.
>In file "C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 14.
>In file "C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_run.m" (v1148), function "run_job" at line 276.
>In file "C:\Users\andre\Documents\Software_fMRI\spm12\toolbox\cat12\cat_run.m" (v1148), function "cat_run" at line 155.
>
>The following modules did not run:
>Failed: CAT12: Segmentation
>
>>>
>
>
>
|
