On Wed, 9 Nov 2016 11:28:33 +0100, Matthieu Vanhoutte <[log in to unmask]> wrote:
>Dear Christian,
>
>Sorry I was mistaken about the context, because my problem occurs during
>CAT_segmentation (not longitudinal) but the error result was the same: PC
>seemed to be stucked in step "Quality check: Developer display mode!" and
>Matlab was still busy but nothing was done.
Please do not use the developer mode...
Best,
Christian
>
>I ran it under Ubuntu linux with last release of CAT12 and Matlab 2014a.
>This problem wasn't observed on my macbook.
>
>Best regards,
>Matthieu
>
>2016-11-09 10:59 GMT+01:00 Matthieu Vanhoutte <[log in to unmask]>:
>
>> Dear Christian,
>>
>> I replied to a former mail posted on mailing list below. I ran it under
>> Ubuntu linux with last release of CAT12 and Matlab 2014a.
>>
>> Best regards,
>> Matthieu
>>
>> ------------------------------------------------------------
>> -----------------------------------------------------
>>
>> Dear Christian and colleagues,
>>
>>
>> I am trying to run CAT12 longitudinal segmentation with surface option but
>> it appears to be stalling (with no error message) on the first subject's
>> second scan. Output is shown below. Running on a linux red hat server,
>> matlab 2014a, CAT 12 r993, and with SPM12 v6685. We've been able to run
>> this same pipeline but without the surface output just fine. The final
>> line in this output is "Developer display mode!" and Matlab continues to
>> indicate as "Busy". Any suggestions would be appreciated! Sincerely - Ryan
>>
>>
>> ------------------------------------
>>
>> >> surf_long_091216
>> Initialising batch system... done.
>>
>>
>> ------------------------------------------------------------------------
>> Running job #1
>> ------------------------------------------------------------------------
>> Running 'Segment longitudinal data'
>>
>>
>> ------------------------------------------------------------------------
>> Running job #2
>> ------------------------------------------------------------------------
>> Running 'Longitudinal Rigid Registration'
>> Estimated noise sd for "/Volumes/Vol6/data/VBM_long/rjh_surf/_011_bravo.nii,1"
>> = 40.8976
>> Estimated noise sd for "/Volumes/Vol6/data/VBM_long/
>> rjh_surf/_011rescan_bravo.nii,1" = 39.908
>> APP:
>> Initialize 5s
>> Estimate background 2s
>> Initial correction 7s
>> Refine background 4s
>> Final correction 6s
>> Background correction 1s
>> Final scaling 2s
>> 35s
>> Done 'Longitudinal Rigid Registration'
>> Running 'CAT12: Segmentation'
>>
>> ------------------------------------------------------------------------
>> CAT12 r993: ./Vol6/data/VBM_long/rjh_surf/avg__011_bravo.nii
>> ------------------------------------------------------------------------
>> SANLM denoising (NCstr=Inf): 22s
>> APP: Rough bias correction:
>> Initialize 5s
>> Estimate background 2s
>> Initial correction 8s
>> Refine background 4s
>> Final correction 6s
>> Background correction 1s
>> Final scaling 2s
>> 28s
>> Coarse affine registration 5s
>> Affine registration 5s
>> SPM preprocessing 1: 88s
>> SPM preprocessing 2: 98s
>> Global intensity correction: 20s
>> SANLM noise correction: 4s
>> Local adaptive segmentation (LASstr=0.50):
>> Prepare maps 5s
>> Prepare partitions 2s
>> Prepare segments 25s
>> Estimate local tissue thresholds 65s
>> SANLM noise correction for LAS: 4s
>> 100s
>> ROI segmentation (partitioning):
>> Atlas -> subject space 10s
>> Major structures 9s
>> Ventricle detection 16s
>> NO WMH detection (CSF ~8%) 0s
>> Closing of deep structures 2s
>> Side alignment 7s
>> Final corrections 3s
>> 47s
>> Skull-stripping using graph-cut (gcutstr=0.50):
>> WM initialisation 6s
>> GM region growing 3s
>> GM-CSF region growing 7s
>> CSF region growing 6s
>> Ventricle closing 3s
>> 25s
>> Amap using initial SPM12 segmentations (MRF filter strength 0.06): MRF
>> priors: alpha 0.221 0.508 0.2 36s
>> 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): 4s
>> Dartel registration:
>> 227s
>> Write result maps: 13s
>> ROI estimation:
>> Data mapping to normalized space 19s
>> ROI estimation of 'hammers' atlas 4s
>> ROI estimation of 'neuromorphometrics' atlas 7s
>> ROI estimation of 'lpba40' atlas 7s
>> 37s
>> Quality check: 6s
>> Print 'Graphics' figure to:
>> /Volumes/Vol6/data/VBM_long/rjh_surf/report/catreport_avg__011_bravo.pdf
>>
>> ------------------------------------------------------------------------
>> CAT preprocessing takes 12 minute(s) and 35 second(s).
>> Image Quality Rating (IQR): 86.17% (B)
>> Segmentations are saved in /Volumes/Vol6/data/VBM_long/rjh_surf/mri
>> Reports are saved in /Volumes/Vol6/data/VBM_long/rjh_surf/report
>> Labels are saved in /Volumes/Vol6/data/VBM_long/rjh_surf/label
>> ------------------------------------------------------------------------
>>
>> Done 'CAT12: Segmentation'
>> Running 'CAT12: Segmentation'
>>
>> ------------------------------------------------------------------------
>> CAT12 r993: ./Vol6/data/VBM_long/rjh_surf/r_011_bravo.nii
>> ------------------------------------------------------------------------
>> SANLM denoising (NCstr=Inf): 22s
>> APP: Rough bias correction:
>> Initialize 5s
>> Estimate background 2s
>> Initial correction 7s
>> Refine background 4s
>> Final correction 6s
>> Background correction 1s
>> Final scaling 2s
>> 27s
>> Coarse affine registration 5s
>> Affine registration 5s
>> SPM preprocessing 1: 100s
>> SPM preprocessing 2: 101s
>> Global intensity correction: 20s
>> SANLM noise correction: 6s
>> Local adaptive segmentation (LASstr=0.50):
>> Prepare maps 4s
>> Prepare partitions 2s
>> Prepare segments 25s
>> Estimate local tissue thresholds 65s
>> SANLM noise correction for LAS: 5s
>> 102s
>> ROI segmentation (partitioning):
>> Atlas -> subject space 10s
>> Major structures 9s
>> Ventricle detection 13s
>> NO WMH detection (CSF ~9%) 0s
>> Closing of deep structures 2s
>> Side alignment 7s
>> Final corrections 3s
>> 44s
>> Skull-stripping using graph-cut (gcutstr=0.50):
>> WM initialisation 6s
>> GM region growing 3s
>> GM-CSF region growing 7s
>> CSF region growing 6s
>> Ventricle closing 3s
>> 25s
>> Amap using initial SPM12 segmentations (MRF filter strength 0.07): MRF
>> priors: alpha 0.225 0.509 0.2 38s
>> 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): 4s
>> Dartel registration:
>> 226s
>> Write result maps: 1s
>> Surface and thickness estimation:
>> lh:
>> Thickness estimation (0.50 mm³):
>> WM distance: 182s
>> CSF distance: 325s
>> PBT2x thickness: 58s
>> Final Corrections: 636s
>> Create initial surface
>> Largest correction will be 2500\nFixing topological defects of size
>> 1\nFixing topological defects of size 2\nFixing topological defects of size
>> 3\nFixing topological defects of size 4\nFixing topological defects of size
>> 5\nFixing topological defects of size 6\nFixing topological defects of size
>> 7\nFixing topological defects of size 8\nFixing topological defects of size
>> 9\nFixing topological defects of size 10\nFixing topological defects of
>> size 11\nFixing topological defects of size 14\nFixing topological defects
>> of size 15\nFixing topological defects of size 17\nFixing topological
>> defects of size 19\nFixing topological defects of size 20\nFixing
>> topological defects of size 23\nFixing topological defects of size
>> 24\nFixing topological defects of size 25\nFixing topological defects of
>> size 26\nFixing topological defects of size 27\nFixing topological defects
>> of size 28\nFixing topological defects of size 29\nFixing topological
>> defects of size 30\nFixing topological defects of size 31\nFixing
>> topological defects of size 32\nFixing topological defects of size
>> 33\nFixing topological defects of size 34\nFixing topological defects of
>> size 35\nFixing topological defects of size 36\nFixing topological defects
>> of size 37\nFixing topological defects of size 38\nFixing topological
>> defects of size 39\nFixing topological defects of size 40\nFixing
>> topological defects of size 41\nFixing topological defects of size
>> 42\nFixing topological defects of size 43\nFixing topological defects of
>> size 44\nFixing topological defects of size 45\nFixing topological defects
>> of size 46\nFixing topological defects of size 47\nFixing topological
>> defects of size 48\nFixing topological defects of size 49\nFixing
>> topological defects of size 80\nFixing topological defects of size
>> 164\nFixing topological defects of size 165\nFixing topological defects of
>> size 166\nFixing topological defects of size 167\nFixing topological
>> defects of size 168\nFixing topological defects of size 169\nFixing
>> topological defects of size 170\nFixing topological defects of size
>> 171\nFixing topological defects of size 172\nFixing topological defects of
>> size 173\nFixing topological defects of size 174\nFixing topological
>> defects of size 175\nFixing topological defects of size 176\nFixing
>> topological defects of size 177\nFixing topological defects of size
>> 178\nFixing topological defects of size 179\nFixing topological defects of
>> size 180\nFixing topological defects of size 181\nFixing topological
>> defects of size 182\nFixing topological defects of size 183\nFixing
>> topological defects of size 184\n
>> 253s
>> 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 3505 adjustments.
>> Extracting component with largest number of vertices...
>> Vertices: 836702 Triangles: 1673400
>> 267s
>> Reduce surface to 100000 faces:
>> Resampled into 304306 polygons.\n
>> Extract largest of 111 components.\n
>> Done \n
>> 24s
>> Topology correction and surface refinement
>> find_selfintersections: .......................................................\n13
>> topological defects\n16 self intersection(s) to repair\nPost-patch: 3 self
>> intersection(s) remaining\n\nResampled into 204776 polygons.\n
>> \n
>> Resampled into 305078 polygons.\n
>> \n
>> 226s
>> Spherical mapping with areal smoothing
>> Done \n
>> 219s
>> Spherical registration 275s
>> Thickness / Depth mapping 1s
>> rh:
>> Thickness estimation (0.50 mm³):
>> WM distance: 214s
>> CSF distance: 647s
>> PBT2x thickness: 67s
>> Final Corrections: 1017s
>> Create initial surface
>> Largest correction will be 2500\nFixing topological defects of size
>> 1\nFixing topological defects of size 2\nFixing topological defects of size
>> 3\nFixing topological defects of size 4\nFixing topological defects of size
>> 5\nFixing topological defects of size 6\nFixing topological defects of size
>> 7\nFixing topological defects of size 8\nFixing topological defects of size
>> 9\nFixing topological defects of size 11\nFixing topological defects of
>> size 14\nFixing topological defects of size 15\nFixing topological defects
>> of size 16\nFixing topological defects of size 21\nFixing topological
>> defects of size 22\nFixing topological defects of size 23\nFixing
>> topological defects of size 24\nFixing topological defects of size
>> 25\nFixing topological defects of size 26\nFixing topological defects of
>> size 27\nFixing topological defects of size 28\nFixing topological defects
>> of size 29\nFixing topological defects of size 30\nFixing topological
>> defects of size 31\nFixing topological defects of size 32\nFixing
>> topological defects of size 33\nFixing topological defects of size
>> 34\nFixing topological defects of size 35\nFixing topological defects of
>> size 36\nFixing topological defects of size 37\nFixing topological defects
>> of size 38\nFixing topological defects of size 39\nFixing topological
>> defects of size 40\nFixing topological defects of size 41\nFixing
>> topological defects of size 42\nFixing topological defects of size
>> 43\nFixing topological defects of size 48\nFixing topological defects of
>> size 75\nFixing topological defects of size 76\nFixing topological defects
>> of size 77\nFixing topological defects of size 78\nFixing topological
>> defects of size 79\nFixing topological defects of size 80\nFixing
>> topological defects of size 81\nFixing topological defects of size
>> 82\nFixing topological defects of size 83\nFixing topological defects of
>> size 84\nFixing topological defects of size 85\nFixing topological defects
>> of size 86\nFixing topological defects of size 87\nFixing topological
>> defects of size 88\nFixing topological defects of size 89\nFixing
>> topological defects of size 90\nFixing topological defects of size
>> 91\nFixing topological defects of size 92\nFixing topological defects of
>> size 93\nFixing topological defects of size 94\nFixing topological defects
>> of size 95\nFixing topological defects of size 735\n
>> 264s
>> 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 7214 adjustments.
>> Extracting component with largest number of vertices...
>> Vertices: 838314 Triangles: 1676624
>> 278s
>> Reduce surface to 100000 faces:
>> Resampled into 303468 polygons.\n
>> Extract largest of 173 components.\n
>> Done \n
>> 23s
>> Topology correction and surface refinement
>> find_selfintersections: .......................................................\n12
>> topological defects\n33 self intersection(s) to repair\nPost-patch: 1 self
>> intersection(s) remaining\n\nResampled into 206070 polygons.\n
>> \n
>> Resampled into 303944 polygons.\n
>> \n
>> 221s
>> Spherical mapping with areal smoothing
>> Done \n
>> 218s
>> Spherical registration 274s
>> Thickness / Depth mapping 1s
>> Display thickness: /Volumes/Vol6/data/VBM_long/
>> rjh_surf/surf/lh.thickness.r_011_bravo
>> Display thickness: /Volumes/Vol6/data/VBM_long/
>> rjh_surf/surf/rh.thickness.r_011_bravo
>> Surface and thickness estimation: 3718s
>> ROI estimation:
>> Data mapping to normalized space 33s
>> ROI estimation of 'hammers' atlas 6s
>> ROI estimation of 'neuromorphometrics' atlas 11s
>> ROI estimation of 'lpba40' atlas 9s
>> 60s
>> Quality check: 6s
>> Developer display mode!
>>
>>
>> 2016-11-09 10:54 GMT+01:00 Christian Gaser <[log in to unmask]>:
>>
>>> Dear Matthieu,
>>>
>>> On Mon, 7 Nov 2016 14:02:15 +0000, Matthieu <[log in to unmask]>
>>> wrote:
>>>
>>> >Hello,
>>> >
>>> >I have exactly the same problem but just running CAT_Segment data with
>>> surface data activated... I am working also on Linux Ubuntu.
>>>
>>> Which problem exactly? And which CAT12 version you are using?
>>>
>>> Best,
>>>
>>> Christian
>>>
>>> >
>>> >Anyone would have an idea ?
>>> >
>>> >Best regards,
>>> >Matthieu
>>>
>>>
>>>
>>
>
|
