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[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:
------------------------------------------------------------ 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.------------
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.
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
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___ ____ __ __
/ __)( _ \( \/ )
\__ \ )___/ ) ( 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
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