Dear Matthieu,
is this error only occurring for this data set? The error message points do an issue with writing the surface gifti data...
Best,
Christian
On Sun, 6 Jan 2019 20:20:11 +0100, Matthieu Vanhoutte <[log in to unmask]> wrote:
>Dear Christian,
>
>Could you help me about the previous warning below ?
>
>Best,
>Matthieu
>
>> Le 23 déc. 2018 à 21:37, Matthieu Vanhoutte <[log in to unmask]> a écrit :
>>
>> Dear CAT’s experts,
>>
>> I got a CAT12 warning during the segmentation and it seems that it causes error when trying to visualize surface data:
>>
>>
>> < M A T L A B (R) >
>> Copyright 1984-2017 The MathWorks, Inc.
>> R2017a (9.2.0.538062) 64-bit (maci64)
>> February 23, 2017
>>
>>
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com <http://www.mathworks.com/>.
>>
>> CAT parallel processing with MATLAB PID: 56009
>>
>> ------------------------------------------------------------------------
>> CAT12.5 r1364: 1/1: CAT12/sub-002S5018_T1w.nii
>> ------------------------------------------------------------------------
>> SANLM denoising (medium): 29s
>> Internal resampling (1.20x1.00x1.00mm > 1.00x1.00x1.00mm): 2s
>> APP: Rough bias correction:
>> Initialize 9s
>> Estimate background 30s
>> Initial correction 19s
>> Refine background 11s
>> Final correction 7s
>> Background correction 1s
>> Final scaling 3s
>> 81s
>> Coarse affine registration 9s
>> Affine registration 7s
>> SPM preprocessing 1 (estimate 1): 13s
>> SPM preprocessing 1 (estimate 2): 98s
>> SPM preprocessing 1 (estimate skull-stripped): 97s
>> SPM preprocessing 1 (estimate skull-stripped): 75s
>> SPM preprocessing 2 (write):
>> Write Segmentation 18s
>> Update Segmentation 45s
>> Update Skull-Stripping 7s
>> Update probability maps 8s
>> 78s
>> Global intensity correction: 24s
>> SANLM denoising after intensity normalization (medium): 16s
>> Fast Shooting registration 49s
>> Local adaptive segmentation (LASstr=0.50):
>> Prepare maps 4s
>> Prepare partitions 2s
>> Prepare segments (LASmod = 1.00) 16s
>> Estimate local tissue thresholds (WM) 17s
>> Estimate local tissue thresholds (GM) 20s
>> Estimate local tissue thresholds (CSF/BG) 5s
>> Intensity transformation 69s
>> SANLM denoising after LAS (medium) 18s
>> 18s
>> ROI segmentation (partitioning):
>> Atlas -> subject space 10s
>> Major structures 5s
>> Ventricle detection 10s
>> Blood vessel detection 11s
>> WMH detection (WMHCstr=0.50 > WMHCstr'=0.50) 29s
>> Manual stroke lesion detection 0s
>> Closing of deep structures 2s
>> Side alignment 4s
>> Final corrections 5s
>> 75s
>> Blood vessel correction (BVCstr=0.50): 2s
>> Amap using initial SPM12 segmentations (MRF filter strength 0.06): 17s
>> AMAP peaks: [CSF,GM,WM] = [0.45±0.08,0.71±0.07,0.96±0.05]
>> Final cleanup (gcutstr=0.23):
>> Level 1 cleanup (ROI estimation) 4s
>> Level 1 cleanup (brain masking) 2s
>> Level 2 cleanup (CSF correction) 1s
>> Level 3 cleanup (CSF/WM PVE) 2s
>> 9s
>>
>>
>> Dartel registration with 1.50 mm on a 1.50 mm Template:
>> Template: "/matlab/spm12/toolbox/cat12/templates_1.50mm/Template_1_IXI555_MNI152.nii"
>> 1 | 0.1436 | 457208 0 457208 0.000
>> 2 | 0.1187 | 377833 19830 397663 0.000
>> 3 | 0.1134 | 361070 27562 388631 0.000
>> 4 | 0.1121 | 357001 15403 372404 0.000
>> 5 | 0.1026 | 326658 33935 360593 0.000
>> 6 | 0.1011 | 321857 36864 358721 0.000
>> 7 | 0.1011 | 322094 19295 341389 0.000
>> 8 | 0.0921 | 293440 37119 330559 0.000
>> 9 | 0.0912 | 290482 38694 329176 0.000
>> 10 | 0.0913 | 290628 20193 310821 0.000
>> 11 | 0.0823 | 262013 37932 299944 0.000
>> 12 | 0.0815 | 259445 39005 298450 0.000
>> 13 | 0.0819 | 260909 20499 281408 0.000
>> 14 | 0.0741 | 235957 35520 271477 0.000
>> 15 | 0.0731 | 232846 37035 269881 0.000
>> 16 | 0.0728 | 231930 38939 270869 0.000
>> 17 | 0.0724 | 230649 39399 270048 0.000
>> 18 | 0.0721 | 229712 40143 269854 0.000
>> 193s
>> Jacobian determinant (RMS): 0.119812
>> Template Matching: 0.072136
>> Write result maps: 19s
>> Surface and thickness estimation:
>> lh:
>> Thickness estimation (0.50 mm³):
>> WM distance: 36s
>> CSF distance: 31s
>> PBT2x thickness: 19s
>> 95s
>> 98s
>> Create initial surface 37s
>> Topology correction and surface refinement: 59s
>> Refine central surface 63s
>> Correction of central surface in highly folded areas 2 3s
>> Spherical mapping with areal smoothing 140s
>> Spherical registration 272s
>> Surface Euler number: -10
>> Overall size of topology defects: 831
>> [Warning: A value of class "int32" was indexed with no subscripts specified.
>> Currently the result of this operation is the indexed value itself, but in a
>> future release, it will be an error.]
>> [> In gifti/subsref (line 45)
>> In cat_surf_createCS (line 861)
>> In cat_main (line 1822)
>> In cat_run_job1070 (line 721)
>> In cat_run_newcatch (line 16)
>> In cat_run>run_job (line 398)
>> In cat_run (line 161)]
>>
>> Then when trying to visualize central surface with the « Display Surface Results » I got this error:
>>
>> Warning: A value of class "int32" was indexed with no subscripts specified. Currently the result of this operation is the
>> indexed value itself, but in a future release, it will be an error.
>> > In gifti/subsref (line 45)
>> In cat_surf_info (line 438)
>> In cat_surf_results (line 357)
>> In cat_surf_results>select_data (line 1648)
>> Warning: A value of class "int32" was indexed with no subscripts specified. Currently the result of this operation is the
>> indexed value itself, but in a future release, it will be an error.
>> > In gifti/subsref (line 45)
>> In spm_mesh_adjacency (line 15)
>> In cat_surf_results (line 382)
>> In cat_surf_results>select_data (line 1648)
>> Error using cat_surf_results (line 415)
>> No data in surfaces found.
>>
>> Error in cat_surf_results>select_data (line 1648)
>> cat_surf_results('disp', H.S{1}.name, H.S{2}.name);
>>
>> Error while evaluating DestroyedObject Callback.
>>
>> Index exceeds matrix dimensions.
>>
>> Error in cat_surf_results (line 317)
>> [pth{1}, nm1, ext1] = spm_fileparts(H.S{1}.name(1, :));
>>
>> Error in cat_surf_results>select_data (line 1648)
>> cat_surf_results('disp', H.S{1}.name, H.S{2}.name);
>>
>> Error while evaluating DestroyedObject Callback.
>>
>> Many thanks in advance for your feedback.
>>
>> Best,
>> Matt
>
>
