Dear Christian,
Could you please provide help with CAT12?
Segmentation keeps crashing with one particular T1 image although it worked fine with many other images. SPM12's Segmentation function, on the other hand, has no problem with this image.
Below is the terminal output with the "warning" lines highlighted. Would you be able to advise how to get around this problem?
Many thanks,
Kie Woo
CAT12 r938: ./Image.nii
------------------------------------------------------------------------
SANLM denoising (NCstr=Inf): 295s
APP: Rough bias correction:
Initialize
9s
Estimate background
8s
Initial correction
19s
Refine background 11s
Final correction
16s
Background correction
1s
Final scaling 4s
68s
Coarse affine registration
12s
Affine registration
15s
SPM preprocessing 1:
192s
SPM preprocessing 2:
242s
Global intensity correction: 34s
SANLM noise correction: 5s
Local adaptive segmentation
(LASstr=0.50):
Prepare maps
2s
Prepare partitions 3s
Prepare segments
6s
Estimate local tissue thresholds 312s
SANLM noise correction for LAS: 8s
331s
ROI segmentation (partitioning):
Atlas -> subject space
6s
Major structures 1s
Ventricle detection
3s
NO WMH detection (to noisy ~0.18) 0s
Closing of deep structures 1s
Side alignment
3s
Final corrections
3s
17s
Skull-stripping using graph-cut
(gcutstr=0.50):
WM initialisation
[@Warning: WARNING: cat_vol_morph - lab - no object!]@
[@> In cat_vol_morph at 119
In cat_main_gcut at 93
In cat_main at 845
In cat_run_job at 541
In cat_run_newcatch at 13
In cat_run>run_job at 246
In cat_run at 154
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]@
2s
2s
Amap using initial SPM12 segmentations
(MRF filter strength 0.07): MRF priors: alpha 1.000 0.000 0.000
Final Mean*Std: 0.663*0.299 -0.340*0.112 -0.340*0.030
Weighted MRF beta -nan
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 1s
Final cleanup (gcutstr=0.50):
Level 1 cleanup (ROI estimation) 1s
Level 1 cleanup (brain masking) [@Warning:
WARNING: cat_vol_morph - lab - no object!]@
[@> In cat_vol_morph at 119
In cat_vol_morph at 107
In cat_main_cleanup at 58
In
cat_main at 965
In cat_run_job at 541
In cat_run_newcatch at 13
In cat_run>run_job at 246
In cat_run at 154
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]@
------------------------------------------------------------------------
CAT Preprocessing error:
MATLAB:dimagree: ./Image.nii
------------------------------------------------------------------------
Matrix dimensions must agree.
------------------------------------------------------------------------
59 - cat_main_cleanup
965 - cat_main
541 - cat_run_job
13 - cat_run_newcatch
246 - run_job
154 - cat_run
29 - cfg_run_cm
1688 - local_runcj
959 - cfg_util
458 - fill_run_job
247 - spm_jobman
------------------------------------------------------------------------
Print 'Graphics' figure to:
/Path/report/catreport_Image.pdf
Failed
'CAT12: Segmentation'
Error using &
Matrix dimensions must agree.
In file "/SPMpath/spm/toolboxes/CAT/cat12_v938/cat_main_cleanup.m"
(???), function "cat_main_cleanup" at line 59.
In file
"/SPMpath/spm/toolboxes/CAT/cat12_v938/cat_main.m" (v928), function
"cat_main" at line 965.
In file
"/SPMpath/spm/toolboxes/CAT/cat12_v938/cat_run_job.m" (v936),
function "cat_run_job" at line 541.
In file
"/SPMpath/spm/toolboxes/CAT/cat12_v938/cat_run_newcatch.m" (???),
function "cat_run_newcatch" at line 13.
In file
"/SPMpath/spm/toolboxes/CAT/cat12_v938/cat_run.m" (v936), function "run_job"
at line 246.
In file
"/SPMpath/spm/toolboxes/CAT/cat12_v938/cat_run.m" (v936), function
"cat_run" at line 154.
The following modules did not run:
Failed: CAT12: Segmentation
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