| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153 |
- ------------------------------------------------------------------------
- CAT12.8.1 r2040: 1/1: ./ses-1/sub-0027449_ses-1_acq-inv1_run-1_T1w.n
- ------------------------------------------------------------------------
- SANLM denoising (medium): 242s
- APP: Rough bias correction:
- Initialize 9s
- Estimate background 9s
- Initial correction 8s
- Refine background 5s
- Final correction 6s
- Final scaling 11s
- 57s
- Correct center-of-mass 2s
- Affine registration 26s
- SPM preprocessing 1 (estimate 1 - TPM registration): 30s
- SPM preprocessing 1 (estimate 2): 47s
- ----------------------------------------------------------------------------
- WARNING 01: cat_run_job1639:nonT1contrast
- A non-T1 contrast was detected and the NEW EXPERIMENTAL
- PIPELINE is used! If it is was a high-resolution T1 image,
- the initial segmentation might have failed, probably due
- to alignment problems (please check the image orientation).
- ----------------------------------------------------------------------------
- SPM preprocessing 2 (write):
- Write Segmentation 26s
- Update segmentation 44s
- Update skull-stripping 21s
- Update probability maps 2s
- Update registration 32s
- 125s
- Global intensity correction: SANLM denoising after intensity normalization (medium): 61s
- ------------------------------------------------------------------------
- NOTE 01: cat_main:skipLAS
- Skip LAS due to image contrast. Use global normalization.
- ------------------------------------------------------------------------
- 134s
- SANLM denoising after LAS (medium) 107s
- 168s
- --- Update Ym and Ymi ---
- ROI segmentation (partitioning):
- Atlas -> subject space 7s
- Major structures 1s
- Ventricle detection 2s
- Blood vessel detection 1s
- Manual stroke lesion detection 0s
- Closing of deep structures 0s
- Side alignment 1s
- Final corrections 7s
- 18s
- Amap using initial SPM12 segmentations (MRF filter strength 0.07): 66s
- AMAP peaks: [0.940.05,0.350.09,0.640.05]
- --- Update Ym and Ymi ---
- Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
- Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"
- 1 | 2.50 | 0.0897 0.0000 0.0897 | 32.0000
- 2 | 2.50 | 0.0842 0.0020 0.0862 | 29.4886
- 3 | 2.50 | 0.0825 0.0031 0.0856 | 26.9772
- 4 | 2.50 | 0.0816 0.0036 0.0852 | 24.6107
- 5 | 2.50 | 0.0809 0.0040 0.0849 | 22.6548
- 6 | 2.50 | 0.0803 0.0042 0.0845 | 20.6989
- 7 | 2.50 | 0.0796 0.0044 0.0840 | 18.9688
- 8 | 2.50 | 0.0790 0.0046 0.0836 | 17.4455
- 9 | 2.50 | 0.0783 0.0048 0.0831 | 15.9223
- 10 | 2.50 | 0.0776 0.0050 0.0826 | 14.6627
- 11 | 2.50 | 0.0769 0.0052 0.0822 | 13.4764
- 12 | 2.50 | 0.0762 0.0054 0.0816 | 12.3015
- 13 | 2.50 | 0.0755 0.0056 0.0811 | 11.3776
- 14 | 2.50 | 0.0748 0.0058 0.0806 | 10.4537
- 15 | 2.25 | 0.0756 0.0061 0.0817 | 9.5920
- 16 | 2.25 | 0.0714 0.0083 0.0797 | 8.8725
- 17 | 2.25 | 0.0695 0.0091 0.0786 | 8.1530
- 29 | 2.00 | 0.0696 0.0042 0.0738 | 3.3283
- 30 | 2.00 | 0.0620 0.0077 0.0697 | 3.1221
- 31 | 2.00 | 0.0595 0.0088 0.0683 | 2.9160
- 43 | 1.75 | 0.0582 0.0052 0.0634 | 1.5785
- 44 | 1.75 | 0.0541 0.0076 0.0616 | 1.5194
- 45 | 1.75 | 0.0527 0.0083 0.0610 | 1.4626
- 57 | 1.50 | 0.0521 0.0063 0.0584 | 1.0900
- 58 | 1.50 | 0.0492 0.0084 0.0575 | 1.0730
- 59 | 1.50 | 0.0483 0.0090 0.0573 | 1.0579
- Shooting registration with 2.50:-0.25:1.50 mm takes: 110s
- Prepare output 12s
- 122s
- Jacobian determinant (RMS): 0.017 0.067 0.110 0.159 0.205 | 0.215512
- Template Matching: 0.090 0.208 0.179 0.158 0.145 | 0.144821
- Write result maps: 45s
- Surface and thickness estimation:
- lh:
- Thickness estimation (0.50 mm):
- WM distance: 15s
- CSF distance: 9s
- PBT2x thickness: 27s
- 55s
- Create initial surface 43s
- Topology correction: 36s
- Surface refinement: 41s
- Reduction of surface collisions with optimization: 35s
- Spherical mapping with areal smoothing 33s
- Spherical registration 194s
- rh:
- Thickness estimation (0.50 mm):
- WM distance: 15s
- CSF distance: 10s
- PBT2x thickness: 27s
- 56s
- Create initial surface 41s
- Topology correction: 36s
- Surface refinement: 32s
- Reduction of surface collisions with optimization: 57s
- Spherical mapping with areal smoothing 33s
- Spherical registration 187s
- Final surface processing results:
- Average thickness (FS): 3.1854 1.0247 mm
- Surface intensity / position RMSE: 0.1329 / 0.1331
- Euler number / defect number / defect size: 46.0 / 32.0 / 1.38%
- Display thickness: /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/surf/lh.thickness.sub-0027449_ses-1_acq-inv1_run-1_T1w
- Display thickness: /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/surf/rh.thickness.sub-0027449_ses-1_acq-inv1_run-1_T1w
- Show surfaces in orthview: /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/sub-0027449_ses-1_acq-inv1_run-1_T1w.nii
- Surface ROI estimation: 1585s
- Surface and thickness estimation takes: 1310s
- ROI estimation in native space:
- ROI estimation of 'cobra' atlas 13s
- ROI estimation of 'neuromorphometrics' atlas 46s
- ROI estimation of 'lpba40' atlas 13s
- ROI estimation of 'hammers' atlas 32s
- ROI estimation of 'thalamus' atlas 2s
- ROI estimation of 'ibsr' atlas 11s
- ROI estimation of 'aal3' atlas 18s
- ROI estimation of 'mori' atlas 28s
- ROI estimation of 'anatomy3' atlas 40s
- ROI estimation of 'julichbrain' atlas 53s
- ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s
- ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 39s
- ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 85s
- ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 128s
- ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s
- Write results 12s
- 543s
- Quality check: 15s
- Print 'Graphics' figure to:
- /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/report/catreport_sub-0027449_ses-1_acq-inv1_run-1_T1w.pdf
- ------------------------------------------------------------------------
- CAT preprocessing takes 46 minute(s) and 22 second(s).
- Image Quality Rating (IQR): 32.21% (F)
- GM volume (GMV): 62.11% (752.49 / 1211.49 ml)
- GM thickness (GMT): 3.19 1.03 mm
- Segmentations are saved in /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/mri
- Reports are saved in /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/report
- Labels are saved in /var/lib/condor/execute/dir_61675/ds/MPG_1/sub-0027449/ses-1/label
- ------------------------------------------------------------------------
|
