Hi all,
I used the cerebromatic toolbox (V1.2) to generate a template for a sample of 66 females that range ages 12-43. When I implement the resulting TPM into CAT12 (v12.6 r1450) segmentation with SPM12 (v7487), Matlab2015a I get the following AMAP estimation error:
------------------------------------------------------------------------
CAT12.6 r1450: 1/66: ./COM_template_affine/CW_0015_461800100001.img
------------------------------------------------------------------------
Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_run_job (line 184)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
SANLM denoising (medium): Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_vol_sanlm_cat_vol_sanlm_filter (line 500)
In cat_vol_sanlm_cat_vol_sanlm_file (line 221)
In cat_vol_sanlm (line 136)
In cat_run_job (line 195)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
16s
Internal resampling (0.86x0.86x1.20mm > 1.00x1.00x1.00mm): Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_vol_imcalc (line 244)
In cat_run_job (line 275)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
2s
APP: Rough bias correction:
Initialize 5s
Estimate background 7s
Initial correction 5s
Refine background 3s
Final correction 4s
Final scaling 6s
36s
Affine registration 9s
Affine registration 7s
SPM preprocessing 1 (estimate 1): 135s
SPM preprocessing 1 (estimate 2): 111s
SPM preprocessing 2 (write):
Write Segmentation 15s
Update Segmentation 42s
Update Skull-Stripping 8s
Update probability maps 0s
65s
Global intensity correction:
WARNING: Inverse tissue contrast!
(BG=185.31, CSF=1436.89, GM=907.29, WM=3.94)
37s
SANLM denoising after intensity normalization (medium): 15s
Fast registration
Dartel registration with 1.50 mm on a 1.50 mm Template:
Template: ".../spm12/toolbox/cat12/templates_1.50mm/Template_1_IXI555_MNI152.nii"
1 | 1.0163 | 3236244 0 3236
70s
76s
Local adaptive segmentation (LASstr=0.50):
Prepare maps 8s
Prepare partitions 1s
Prepare segments (LASmod = 1.00) 29s
Estimate local tissue thresholds (WM) 24s
Estimate local tissue thresholds (GM) 5s
Estimate local tissue thresholds (CSF/BG) 5s
Intensity transformation 74s
SANLM denoising after LAS (medium) 26s
26s
ROI segmentation (partitioning):
Atlas -> subject space 15s
Major structures 9s
Ventricle detection 11s
Blood vessel detection 11s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 41s
Manual stroke lesion detection 0s
Closing of deep structures 4s
Side alignment 11s
Final corrections 6s
108s
Amap using initial SPM12 segmentations (MRF filter strength 0.02): 81s
AMAP peaks: [CSF,GM,WM] = [0.78±0.23,0.29±0.03,0.99±0.01]
------------------------------------------------------------------------
CAT Preprocessing error for CW_0015_461800100001:
------------------------------------------------------------------------
AMAP estimated untypical tissue peaks that point to an
error in the preprocessing before the AMAP segmentation.
------------------------------------------------------------------------
128 - cat_main_amap
405 - cat_main
786 - cat_run_job
15 - cat_run_newcatch
720 - run_job
434 - cat_run
29 - cfg_run_cm
1717 - local_runcj
972 - cfg_util
710 - MenuFileRun_Callback
95 - gui_mainfcn
53 - cfg_ui
------------------------------------------------------------------------
21-May-2019 15:29:02 - Failed 'CAT12: Segmentation'
Reference to a cleared variable cat_err_res.
In file ".../MATLAB/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 56.
In file ".../MATLAB/spm12/toolbox/cat12/cat_run.m" (v1439), function "run_job" at line 720.
In file ".../MATLAB/spm12/toolbox/cat12/cat_run.m" (v1439), function "cat_run" at line 434.
The following modules did not run:
Failed: CAT12: Segmentation
As previously suggested in another thread, I tried changing the APP correction to "light" but then got a different error:
------------------------------------------------------------------------
CAT12.6 r1450: 1/66: ./COM_template_affine/CW_0015_461800100001.img
------------------------------------------------------------------------
Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_run_job (line 184)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
SANLM denoising (medium): Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_vol_sanlm_cat_vol_sanlm_filter (line 500)
In cat_vol_sanlm_cat_vol_sanlm_file (line 221)
In cat_vol_sanlm (line 136)
In cat_run_job (line 195)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
16s
Internal resampling (0.86x0.86x1.20mm > 1.00x1.00x1.00mm): Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_vol_imcalc (line 244)
In cat_run_job (line 275)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
2s
APPs bias correction:
Preparation Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_run_job_APP_SPMinit (line 108)
In cat_run_job (line 299)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_smooth>smooth1 (line 105)
In spm_smooth (line 37)
In cat_run_job_APP_SPMinit (line 162)
In cat_run_job (line 299)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_run_job_APP_SPMinit (line 164)
In cat_run_job (line 299)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
3s
SPM bias correction (samp: 6.00 mm, fwhm: 120 mm) 47s
SPM bias correction (samp: 3.00 mm, fwhm: 60 mm) 120s
Postprocessing Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In nifti/subsasgn>fun (line 109)
In nifti/subsasgn (line 20)
In spm_create_vol>create_vol (line 109)
In spm_create_vol (line 17)
In spm_write_vol (line 83)
In cat_run_job_APP_SPMinit (line 337)
In cat_run_job (line 299)
In cat_run_newcatch (line 15)
In cat_run>run_job (line 720)
In cat_run (line 434)
In cfg_run_cm (line 29)
In cfg_util>local_runcj (line 1717)
In cfg_util (line 972)
In cfg_ui>MenuFileRun_Callback (line 710)
In gui_mainfcn (line 95)
In cfg_ui (line 53)
196s
Coarse affine registration: 9s
Affine registration 6s
SPM preprocessing 1 (estimate 1): 201s
SPM preprocessing 1 (estimate 2): 40s
SPM preprocessing 2 (write):
Write Segmentation 15s
Update Segmentation
------------------------------------------------------------------------
CAT Preprocessing error for CW_0015_461800100001:
------------------------------------------------------------------------
Empty Segmentation:
Possibly the affine registration failed. Please check image orientation.
Tissue class: BG CSF GM WM HDH HDL
Rel. to image volume: 85.83 0.00 0.00 0.00 4.80 9.37
Rel. to brain volume: Inf NaN NaN NaN Inf Inf
Tissue intensity: 10.00 -18.93 -6.60 5.73 8.36 8.90
------------------------------------------------------------------------
101 - cat_main_updateSPM
70 - cat_main
786 - cat_run_job
15 - cat_run_newcatch
720 - run_job
434 - cat_run
29 - cfg_run_cm
1717 - local_runcj
972 - cfg_util
710 - MenuFileRun_Callback
95 - gui_mainfcn
53 - cfg_ui
------------------------------------------------------------------------
21-May-2019 15:39:57 - Failed 'CAT12: Segmentation'
Reference to a cleared variable cat_err_res.
In file ".../MATLAB/spm12/toolbox/cat12/cat_run_newcatch.m" (???), function "cat_run_newcatch" at line 56.
In file ".../MATLAB/spm12/toolbox/cat12/cat_run.m" (v1439), function "run_job" at line 720.
In file ".../MATLAB/spm12/toolbox/cat12/cat_run.m" (v1439), function "cat_run" at line 434.
The following modules did not run:
Failed: CAT12: Segmentation
All of the images are AC oriented so I'm not sure what the issue is or how to find out. This particular subject's image has been used previously in a standard CAT12 segmentation analysis using the standard TPM provided.
I have also tried changing the skull-stripping method to APRG rather than SPM since the CAT12 toolbox suggests it is most accurate but that returned the same Empty segmentation error above.
I'm a novice with all of these tools and would appreciate any help at all, thanks!
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