Dear all,
I have generated tissue priors with CerebroMatic and when I try to segment any image with CAT12 I get the following error message: 'Dimensions of matrices being concatenated are not consistent.'
I am copying the full log below. Note that it gives a warning of inverse tissue contrast that does not appear when I use the original TPM. I have also noticed that the last tissue class (number 6) generated with CerebroMatic is an empty image (all zeros), which is different from the original TPM. Maybe this has something to do with the inverse tissue contrast alert?
Thank you.
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Full log of CAT12 segmentation attempt:
SANLM denoising (medium): 60s
APP: Rough bias correction:
Initialize 15s
Estimate background 12s
Initial correction 12s
Refine background 8s
Final correction 13s
Final scaling 18s
96s
Affine registration 21s
Affine registration 52s
SPM preprocessing 1 (estimate 1): 286s
SPM preprocessing 1 (estimate 2): 94s
SPM preprocessing 2 (write):
Write Segmentation 32s
Update Segmentation 79s
Update Skull-Stripping 123s
Update probability maps 1s
235s
Global intensity correction:
WARNING: Inverse tissue contrast!
(BG=52.27, CSF=121.53, GM=52.27, WM=25.67)
108s
SANLM denoising after intensity normalization (medium): 0s
Fast registration
Dartel registration with 1.50 mm on a 1.50 mm Template:
Template: "C:\software\spm12\toolbox\cat12\templates_1.50mm\Template_1_IXI555_MNI152.nii"
1 | 3.2751 | 10429260 0 10429260 774.996
2 | 3.2486 | 10344908 35476 10380384 587.357
3 | 3.2250 | 10269589 65202 10334791 491.704
4 | 3.1758 | 10113135 100463 10213599 446.259
5 | 3.0971 | 9862466 133686 9996152 406.069
6 | 2.9916 | 9526627 303259 9829887 308.863
97s
110s
Local adaptive segmentation (LASstr=0.50):
Prepare maps 0s
Prepare partitions 3s
Prepare segments (LASmod = 1.00) 11s
Estimate local tissue thresholds (WM) 24s
Estimate local tissue thresholds (GM) 12s
Estimate local tissue thresholds (CSF/BG) 10s
Intensity transformation 65s
SANLM denoising after LAS (medium) 15s
15s
ROI segmentation (partitioning):
Atlas -> subject space 6s
Major structures 0s
Ventricle detection 0s
Blood vessel detection 0s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.50) 0s
Manual stroke lesion detection 0s
Closing of deep structures 0s
Side alignment 0s
Final corrections 5s
12s
Amap using initial SPM12 segmentations (MRF filter strength 0.06): 0s
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CAT Preprocessing error for xxxx:
------------------------------------------------------------------------
Dimensions of matrices being concatenated are not consistent.
------------------------------------------------------------------------
76 - cell2mat
119 - cat_main_amap
405 - cat_main
786 - cat_run_job
15 - cat_run_newcatch
720 - run_job
434 - cat_run
------------------------------------------------------------------------
Error:cat_io_report:dispYoHist: Error in displaying the color histogram of the original image.
Error:cat_io_report:dispYmHist: Error in displaying the color histogram of the processed image.
Error:cat_io_report:dispYp0Hist: Error in displaying the color histogram of the segmented image.
{Index exceeds matrix dimensions.
Error in cat_surf_create_TPM_hull_surface (line 58)
Yb = exp(tpm.dat{1}) + exp(tpm.dat{2}) + exp(tpm.dat{3});
Error in cat_io_report (line 563)
Phull = {cat_surf_create_TPM_hull_surface(job.opts.tpm)};
Error in cat_run_newcatch (line 63)
cat_io_report(job,qa,subj)
Error in cat_run>run_job (line 720)
cat_run_newcatch(job,tpm,subj);
Error in cat_run (line 434)
varargout{1} = run_job(job);
}
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