Dear everyone,
I ran into an error message "[GIFTI] Parsing of XML file" during surface reconstruction as part of the segmentation with CAT12.8.2 r2170 / SPM12 r7771 under Matlab R2021a. See below for the complete message (the same for other subjects). Any ideas what this might refer to? As I don't use the default settings, which might possibly have led to the issue, please find the batch at WeTransfer https://we.tl/t-ETAmdM5pQt
Thank you very much,
Helmut
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CAT12.8.2 r2170: 1/18: ./sxxxxx_struc.img
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SANLM denoising (medium) 77s
Internal resampling (1.00x1.00x1.10mm > 1.00x1.00x1.00mm) 2s
APP: Rough bias correction
Initialize 11s
Estimate background 8s
Initial correction 6s
Refine background 4s
Final correction 5s
Final scaling 5s
47s
Correct center-of-mass 7s
Affine registration 9s
SPM preprocessing 1 (estimate 1 - TPM registration): 88s
SPM preprocessing 1 (estimate 2): 157s
SPM preprocessing 2 (write)
Write Segmentation 22s
Update Segmentation 18s
Update Skull-Stripping 42s
Update probability maps 7s
90s
Global intensity correction 18s
SANLM denoising after intensity normalization (medium) 11s
Fast Optimized Shooting registration 58s
Local adaptive segmentation (LASstr=0.50)
Prepare maps 4s
Prepare partitions 2s
Prepare segments (LASmod = 1.16) 11s
Estimate local tissue thresholds (WM) 19s
Estimate local tissue thresholds (GM) 26s
Intensity transformation 0s
SANLM denoising after LAS (medium) 31s
95s
ROI segmentation (partitioning)
Atlas -> subject space 7s
Major structures 3s
Ventricle detection 10s
Blood vessel detection 9s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.13) 20s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 3s
Final corrections 3s
57s
Blood vessel correction (BVCstr=0.50) 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.06) 23s
AMAP peaks: [CSF,GM,WM] = [0.36±0.05,0.68±0.08,0.98±0.05]
Final cleanup (gcutstr=0.25)
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
Optimized Shooting registration with 2.50:-0.38:1.00 mm (regstr=0.50)
Template: "/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym_1mm/Template_0_GS1mm.nii"
1 | 2.50 | 0.0725 0.0000 0.0725 | 32.0000
2 | 2.50 | 0.0701 0.0011 0.0711 | 29.4886
3 | 2.50 | 0.0693 0.0016 0.0710 | 26.9772
4 | 2.50 | 0.0690 0.0018 0.0708 | 24.6107
5 | 2.50 | 0.0687 0.0020 0.0707 | 22.6548
6 | 2.50 | 0.0684 0.0021 0.0705 | 20.6989
7 | 2.50 | 0.0682 0.0022 0.0703 | 18.9688
8 | 2.50 | 0.0679 0.0022 0.0702 | 17.4455
9 | 2.50 | 0.0677 0.0023 0.0700 | 15.9223
10 | 2.50 | 0.0674 0.0024 0.0698 | 14.6627
11 | 2.50 | 0.0671 0.0025 0.0696 | 13.4764
12 | 2.50 | 0.0668 0.0025 0.0693 | 12.3015
13 | 2.50 | 0.0665 0.0026 0.0691 | 11.3776
14 | 2.50 | 0.0662 0.0027 0.0689 | 10.4537
15 | 2.12 | 0.0660 0.0028 0.0688 | 9.5920
16 | 2.12 | 0.0629 0.0043 0.0672 | 8.8725
29 | 1.75 | 0.0652 0.0020 0.0672 | 3.3283
30 | 1.75 | 0.0580 0.0047 0.0627 | 3.1221
31 | 1.75 | 0.0556 0.0059 0.0614 | 2.9160
43 | 1.38 | 0.0549 0.0034 0.0583 | 1.5785
44 | 1.38 | 0.0497 0.0060 0.0557 | 1.5194
45 | 1.38 | 0.0480 0.0068 0.0548 | 1.4626
57 | 1.00 | 0.0459 0.0051 0.0510 | 1.0900
58 | 1.00 | 0.0427 0.0070 0.0497 | 1.0730
59 | 1.00 | 0.0417 0.0075 0.0492 | 1.0579
Shooting registration with 2.50:-0.38:1.00 mm takes 598s
Prepare output 23s
621s
Jacobian determinant (RMS): 0.010 0.038 0.061 0.094 0.122 | 0.129694
Template Matching: 0.072 0.189 0.167 0.144 0.125 | 0.125069
Write result maps 68s
Surface and thickness estimation
lh:
Thickness estimation (0.50 mm³)
WM distance: 27s
CSF distance: 13s
PBT2x thickness: 49s
95s
Create initial surface 62s[Warning: [GIFTI] Parsing of XML file
./lh.layer4x.sxxxxx_struc.gii
failed.]
[> In read_gifti_file (line 17)
In gifti (line 108)
In cat_surf_fun>cat_surf_evalCS (line 1295)
In cat_surf_fun (line 200)
In cat_surf_createCS2 (line 1084)
In cat_main1639 (line 795)
In cat_run_job1639 (line 1269)
In cat_run_newcatch (line 40)
In cat_run>run_job (line 1170)
In cat_run (line 706)]
Topology correction:
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CAT Preprocessing error for sf85g3_struc:
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Surface file ./lh.central.sxxxxx_struc.gii could not be found due to previous processing errors.
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1882 - loadSurf
1148 - cat_surf_createCS2
795 - cat_main1639
1269 - cat_run_job1639
40 - cat_run_newcatch
1170 - run_job
706 - cat_run
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Print 'Graphics' figure to:
/media/neh27422/TOSHIBA1/Data/MD_Helmut/DataPreproc/CAT12_Var1/Regensburg/AMD/catreport_sf85g3_struc.pdf
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