Dear Feng,
On 23 May 2017, at 3:41, FENG LIU wrote:
> Thanks, Christian
>
>
> So, you mean that the generated files (VBM and SBM) are correct, and I
> can
> directly use them to conduct statistical analyses, right?
Yes, the error occurred after finishing the preprocessing.
Best,
Christian
>
> Best,
> Feng
>
> On Mon, May 22, 2017 at 6:25 PM, Christian Gaser <
> [log in to unmask]> wrote:
>
>> Dear Feng,
>>
>> this is an display error because the default renderer is not
>> available on
>> your server. I assume that the graphical output is suppressed to run
>> jobs
>> in the background. A better way is maybe to use the shell script
>> cat_batch_vbm.sh that allows to distribute the jobs to all available
>> processors and to run the process in the background while all
>> graphical
>> output is saved as PDF file. Please check the help text for more
>> information.
>>
>> Best,
>>
>> Christian
>>
>> On Mon, 22 May 2017 08:35:25 +0800, FENG LIU <[log in to unmask]>
>> wrote:
>>
>>> Dear CAT experts:
>>>
>>> This is the first time that I use the CAT12 toolbox. I used the
>>> server SGE
>>> in my lab to run the CAT12; when I finished the job, I found all the
>>> files
>>> were generated (see attached figures). However, there were error
>>> information that I cannot handle. Could anyone give me some
>>> suggestions?
>>> Any help would be greatly appreciate!
>>>
>>> Best,
>>> Feng
>>>
>>> *All the information were listed below.*
>>> Warning: No display specified. You will not be able to display
>>> graphics
>> on
>>> the screen.
>>> Warning: No window system found. Java option 'MWT' ignored
>>>
>>> < M A T L A B (R) >
>>> Copyright 1984-2010 The MathWorks, Inc.
>>> Version 7.12.0.635 (R2011a) 64-bit (glnxa64)
>>> March 18, 2011
>>>
>>> Warning: Duplicate directory name: /root/matlab.
>>>
>>> To get started, type one of these: helpwin, helpdesk, or demo.
>>> For product information, visit www.mathworks.com.
>>>
>>>
>>> command =
>>>
>>> lf_cat(opt.parameter1)
>>>
>>>
>>> files_in =
>>>
>>> {}
>>>
>>>
>>> files_out =
>>>
>>> {}
>>>
>>>
>>> files_clean =
>>>
>>> {}
>>>
>>>
>>> opt =
>>>
>>> parameter1: [1x68 char]
>>>
>>>
>>> ******************************
>>> Log of the (matlab) job : CAT_10
>>> Started on 19-May-2017 15:28:00
>>> User: root
>>> host : server5.local
>>> system : unix
>>> ******************************
>>>
>>> ********************
>>> The job starts now !
>>> ********************
>>> Initialising batch system... Item 'VBM8 Realign: Reslice', field
>>> 'prog':
>>> Value must be a function or function handle on MATLAB path.
>>> Item 'VBM8 Realign: Reslice', field 'prog': Value must be a function
>>> or
>>> function handle on MATLAB path.
>>> done.
>>>
>>>
>>> ------------------------------------------------------------------------
>>> Running job #1
>>> ------------------------------------------------------------------------
>>> Running 'CAT12: Segmentation'
>>> Warning: Dartel template was changed: Please be aware that ROI
>>> analysis
>> and
>>> other template-specific options cannot be used and ROI output has
>>> been
>>> deselected.
>>>> In cat_run>update_job at 186
>>> In cat_run at 153
>>> In matlabbatch/private/cfg_run_cm at 29
>>> In cfg_util>local_runcj at 1688
>>> In cfg_util at 959
>>> In spm_jobman>fill_run_job at 458
>>> In spm_jobman at 247
>>> In lf_cat at 24
>>> In psom_run_job>sub_eval at 203
>>> In psom_run_job at 125
>>>
>>> ------------------------------------------------------------------------
>>> CAT12 r1059:
>>> ./share/CHIMGEN/T1CAT/010010/co20151122_161744SUNYI.nii
>>> ------------------------------------------------------------------------
>>> SANLM denoising (NCstr=Inf):
>>> 312s
>>> APP: Rough bias correction:
>>> Initialize
>>> 15s
>>> Estimate background
>>> 9s
>>> Initial correction
>>> 24s
>>> Refine background
>>> 15s
>>> Final correction
>>> 21s
>>> Background correction
>>> 2s
>>> Final scaling
>>> 8s
>>> Coarse
>>> affine registration 117s
>>> Affine registration
>>> 78s
>>> SPM preprocessing 1:
>>> 723s
>>> SPM preprocessing 2:
>>> 425s
>>> Global intensity correction:
>>> 77s
>>> SANLM noise correction:
>>> 21s
>>> Local adaptive segmentation (LASstr=0.50):
>>> Prepare maps
>>> 19s
>>> Prepare partitions
>>> 7s
>>> Prepare segments
>>> 73s
>>> Estimate local tissue thresholds
>>> 188s
>>> SANLM noise correction for LAS:
>>> 23s
>>> 311s
>>> ROI segmentation (partitioning):
>>> Atlas -> subject space
>>> 32s
>>> Major structures
>>> 23s
>>> Ventricle detection
>>> 36s
>>> NO WMH detection (CSF ~9%)
>>> 0s
>>> Closing of deep structures
>>> 7s
>>> Side alignment
>>> 18s
>>> Final corrections
>>> 6s
>>> 122s
>>> Skull-stripping using graph-cut (gcutstr=1.00):
>>> WM initialisation
>>> 16s
>>> GM region growing
>>> 6s
>>> GM-CSF region growing
>>> 15s
>>> CSF region growing
>>> 15s
>>> Ventricle closing
>>> 10s
>>> 62s
>>> Amap using initial SPM12 segmentations (MRF filter strength 0.06):
>>> MRF
>>> priors: alpha 0.165 0.524 0.3 125s
>>> Final cleanup (gcutstr=0.50):
>>> Level 1 cleanup (ROI estimation)
>>> 17s
>>> Level 1 cleanup (brain masking)
>>> 8s
>>> Level 2 cleanup (CSF correction)
>>> 8s
>>> Level 3 cleanup (CSF/WM PVE)
>>> 5s
>>> 38s
>>> Internal WMH correction for spatial normalization (WMHCstr=0.50):
>>> 10s
>>> Dartel registration:
>>> 817s
>>> Write result maps:
>>> 126s
>>> Surface and thickness estimation:
>>> lh:
>>> Thickness estimation (0.50 mm³):
>>> WM distance:
>>> 171s
>>> CSF distance:
>>> 176s
>>> PBT2x thickness:
>>> 93s
>>> Final Corrections:
>>> 482s
>>> Create initial surface
>>> Largest correction will be 10000
>>> Fixing topological defects of size 1
>>> Fixing topological defects of size 2
>>> Fixing topological defects of size 3
>>> Fixing topological defects of size 6
>>> Fixing topological defects of size 8
>>> Fixing topological defects of size 24
>>> Fixing topological defects of size 25
>>> Fixing topological defects of size 26
>>> Fixing topological defects of size 27
>>> Fixing topological defects of size 28
>>> Fixing topological defects of size 29
>>> Fixing topological defects of size 30
>>> Fixing topological defects of size 31
>>> Fixing topological defects of size 32
>>> Fixing topological defects of size 33
>>> Fixing topological defects of size 34
>>> Fixing topological defects of size 35
>>> Fixing topological defects of size 36
>>> Fixing topological defects of size 37
>>> Fixing topological defects of size 38
>>> Fixing topological defects of size 39
>>> Fixing topological defects of size 40
>>> Fixing topological defects of size 41
>>> Fixing topological defects of size 42
>>> Fixing topological defects of size 43
>>> Fixing topological defects of size 44
>>> Fixing topological defects of size 129
>>> Fixing topological defects of size 130
>>> Fixing topological defects of size 131
>>> Fixing topological defects of size 132
>>> Fixing topological defects of size 133
>>> Fixing topological defects of size 134
>>> Fixing topological defects of size 135
>>> Fixing topological defects of size 136
>>> Fixing topological defects of size 137
>>> Fixing topological defects of size 138
>>> Fixing topological defects of size 139
>>> Fixing topological defects of size 140
>>> Fixing topological defects of size 141
>>> Fixing topological defects of size 142
>>> Fixing topological defects of size 143
>>> Fixing topological defects of size 144
>>> Fixing topological defects of size 145
>>> Fixing topological defects of size 146
>>> Fixing topological defects of size 147
>>> Fixing topological defects of size 148
>>> Fixing topological defects of size 149
>>>
>>> 425s
>>> 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 1433 adjustments.
>>> Extracting component with largest number of vertices...
>>> Vertices: 623642 Triangles: 1247280
>>> 454s
>>> Reduce surface to 100000 faces:
>>> Resampled into 261926 polygons.
>>> Extract largest of 121 components.
>>> Done
>>> 65s
>>> Topology correction and surface refinement
>>> find_selfintersections:
>>> .......................................................
>>> 15 topological defects
>>> find_selfintersections:
>>> .......................................................
>>> 54 self intersection(s) to repair
>>> Post-patch: 1 self intersection(s) remaining
>>>
>>> Resampled into 166394 polygons.
>>>
>>> Resampled into 246744 polygons.
>>>
>>> 666s
>>> Spherical mapping with areal smoothing
>>> Done
>>>
>>> 584s
>>> Spherical registration
>>> 953s
>>> Thickness / Depth mapping
>>> 2s
>>> rh:
>>> Thickness estimation (0.50 mm³):
>>> WM distance:
>>> 157s
>>> CSF distance:
>>> 166s
>>> PBT2x thickness:
>>> 90s
>>> Final Corrections:
>>> 457s
>>> Create initial surface
>>> Largest correction will be 10000
>>> Fixing topological defects of size 1
>>> Fixing topological defects of size 2
>>> Fixing topological defects of size 3
>>> Fixing topological defects of size 5
>>> Fixing topological defects of size 6
>>> Fixing topological defects of size 7
>>> Fixing topological defects of size 18
>>> Fixing topological defects of size 34
>>> Fixing topological defects of size 700
>>> Fixing topological defects of size 701
>>> Fixing topological defects of size 702
>>> Fixing topological defects of size 703
>>> Fixing topological defects of size 704
>>> Fixing topological defects of size 705
>>> Fixing topological defects of size 706
>>> Fixing topological defects of size 707
>>> Fixing topological defects of size 708
>>> Fixing topological defects of size 709
>>> Fixing topological defects of size 710
>>> Fixing topological defects of size 711
>>> Fixing topological defects of size 712
>>> Fixing topological defects of size 713
>>> Fixing topological defects of size 714
>>> Fixing topological defects of size 715
>>> Fixing topological defects of size 716
>>> Fixing topological defects of size 717
>>> Fixing topological defects of size 718
>>> Fixing topological defects of size 719
>>> Fixing topological defects of size 720
>>>
>>> 194s
>>> 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 423 adjustments.
>>> Extracting component with largest number of vertices...
>>> Vertices: 627098 Triangles: 1254192
>>> 224s
>>> Reduce surface to 100000 faces:
>>> Resampled into 266946 polygons.
>>> Extract largest of 157 components.
>>> Done
>>> 61s
>>> Topology correction and surface refinement
>>> find_selfintersections:
>>> .......................................................
>>> 15 topological defects
>>> 48 self intersection(s) to repair
>>> Post-patch: 1 self intersection(s) remaining
>>>
>>> Resampled into 169932 polygons.
>>>
>>> Resampled into 250588 polygons.
>>>
>>> 599s
>>> Spherical mapping with areal smoothing
>>> Done
>>>
>>> 633s
>>> Spherical registration
>>> 930s
>>> Thickness / Depth mapping
>>> 2s
>>> Display thickness:
>>> /gpfs2/groupYU/share/CHIMGEN/T1CAT/010010/surf/lh.thickness.co20151122_
>> 161744SUNYI
>>> Display thickness:
>>> /gpfs2/groupYU/share/CHIMGEN/T1CAT/010010/surf/rh.thickness.co20151122_
>> 161744SUNYI
>>> Surface and thickness estimation:
>>> 6231s
>>> Quality check:
>>> 18s
>>> Developer display mode!
>>>
>>> ------------------------------------------------------------------------
>>> *CAT Preprocessing error: MATLAB:hg:propswch:FindObjFailed:
>>> ./share/CHIMGEN/T1CAT/010010/co20151122_161744SUNYI.nii *
>>> ------------------------------------------------------------------------
>>> Bad property value found.
>>> Object Name : figure
>>> Property Name : 'Renderer'.
>>> ------------------------------------------------------------------------
>>> 62 - restorehg
>>> 33 - restore
>>> 282 - LocalPrint
>>> 228 - print
>>> 2303 - cat_main
>>> 614 - cat_run_job
>>> 13 - cat_run_newcatch
>>> 247 - run_job
>>> 155 - cat_run
>>> 29 - cfg_run_cm
>>> 1688 - local_runcj
>>> 959 - cfg_util
>>> 458 - fill_run_job
>>> 247 - spm_jobman
>>> 24 - lf_cat
>>> 203 - sub_eval
>>> 125 - psom_run_job
>>> ------------------------------------------------------------------------
>>> Developer display mode!
>>>
>>> Print 'Graphics' figure to:
>>>
>>> */gpfs2/groupYU/share/CHIMGEN/T1CAT/010010/report/catreport_co20151122_
>> 161744SUNYI.pdf*
>>> *Failed 'CAT12: Segmentation'*
>>> *Error using ==> fill3*
>>> *Vectors must be the same lengths.*
>>> *In file
>>> "/gpfs1/public/software/matlab_toolbox/toolbox/spm12/
>> toolbox/cat12/cat_io_report.m"
>>> (???), function "cat_io_report" at line 418.*
>>> *In file
>>> "/gpfs1/public/software/matlab_toolbox/toolbox/spm12/
>> toolbox/cat12/cat_run_newcatch.m"
>>> (???), function "cat_run_newcatch" at line 63.*
>>> *In file
>>> "/gpfs1/public/software/matlab_toolbox/toolbox/spm12/
>> toolbox/cat12/cat_run.m"
>>> (v1040), function "run_job" at line 247.*
>>> *In file
>>> "/gpfs1/public/software/matlab_toolbox/toolbox/spm12/
>> toolbox/cat12/cat_run.m"
>>> (v1040), function "cat_run" at line 155.*
>>>
>>> *The following modules did not run:*
>>> *Failed: CAT12: Segmentation*
>>>
>>>
>>>
>>> ********************
>>> Something went bad ... the job has FAILED !
>>> The last error message occured was :
>>> Error using ==> MATLABbatch system
>>> Job execution failed. The full log of this run can be found in
>>> MATLAB
>>> command window, starting with the lines (look for the line showing
>>> the
>>> exact #job as displayed in this error message)
>>> ------------------
>>> Running job #1
>>> ------------------
>>>
>>> File at line 0
>>>
>>> ****************
>>> Checking outputs
>>> ****************
>>>
>>> *************************************************
>>> 19-May-2017 18:12:27 : The job has FAILED
>>> Total time used to process the job : 9866.98 sec.
>>> *************************************************
>>>
>>> ans =
>>>
>>> 1
>>>
>>
>>
>>
