Regarding all your missing files: make sure you do not start another instance of Brainstorm while you run CAT. Starting Brainstorm empties the temporary folder $HOME/.brainstorm/tmp, which includes the temporary folder for cat12, causing the process to fail.
I updated the CAT segmentation and import in Brainstorm, it may help as well:
- CAT12: Updated segmentation process and import function (WIP) · brainstorm-tools/brainstorm3@5212b57 · GitHub
- CAT12: Added support for cerebellum surface · brainstorm-tools/brainstorm3@7528573 · GitHub
- CAT: Fix import and keep CAT ouptut in .brainstorm/tmp/cat12 · brainstorm-tools/brainstorm3@56a3cca · GitHub
I did the following:
- Created a new subject (default anatomy: NO, default channel file: NO)
- Right-click on subject folder > Use template > ICBM152
- Delete all the surfaces, keep only the MRI
- Execute the script below:
% Process: Segment MRI with CAT12
sFiles = bst_process('CallProcess', 'process_segment_cat12', [], [], ...
'subjectname', 'CAT12_ICBM152', ...
'nvertices', 15000, ...
'tpmnii', {'', 'Nifti1'}, ...
'sphreg', 1, ...
'extramaps', 1);
Here is the output of CAT in the Matlab command window:
(@CGaser: see the errors about catROI_CAT12_ICBM152.xml)
SPM12: spm_cat12 (vCAT12.7) 19:45:38 - 10/11/2020
========================================================================
_______ ___ _______
| ____/ / _ \ \_ _/ Expert Mode
| |___ / /_\ \ | | Computational Anatomy Toolbox
|____/ /_/ \_\ |_| CAT12.7 - http://www.neuro.uni-jena.de
CAT default file:
C:\Work\Dev\Divers\spm12\toolbox\cat12\cat_defaults.m
------------------------------------------------------------------------
10-Nov-2020 19:45:46 - Running job #1
------------------------------------------------------------------------
10-Nov-2020 19:45:46 - Running 'CAT12: Segmentation (current release)'
External diary log is writen to "of".
Your version of CAT12 is up to date.
------------------------------------------------------------------------
CAT12.7 r1728: 1/1: .\franc\.brainstorm\tmp\cat12\CAT12_ICBM152.nii
------------------------------------------------------------------------
SANLM denoising (medium): 33s
APP: Rough bias correction:
Initialize 5s
Estimate background 4s
Initial correction 7s
Refine background 4s
Final correction 7s
Final scaling 9s
41s
Affine registration 4s
Affine registration 7s
SPM preprocessing 1 (estimate 1):
Final fine affine registration failed.
Use fine affine registration from previous step.
102s
SPM preprocessing 1 (estimate 2): 91s
SPM preprocessing 2 (write):
Write Segmentation 20s
Update Segmentation 28s
Update Skull-Stripping 31s
Update probability maps 6s
84s
Global intensity correction: 13s
SANLM denoising after intensity normalization (medium): 11s
Fast registration 37s
Local adaptive segmentation (LASstr=0.50):
Prepare maps 5s
Prepare partitions 1s
Prepare segments (LASmod = 1.00) 13s
Estimate local tissue thresholds (WM) 15s
Estimate local tissue thresholds (GM) 22s
Estimate local tissue thresholds (CSF/BG) 3s
Intensity transformation 62s
SANLM denoising after LAS (medium) 21s
21s
ROI segmentation (partitioning):
Atlas -> subject space 9s
Major structures 6s
Ventricle detection 15s
Blood vessel detection 10s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 31s
Manual stroke lesion detection 0s
Closing of deep structures 2s
Side alignment 5s
Final corrections 2s
81s
Blood vessel correction (BVCstr=0.50): 1s
Amap using initial SPM12 segmentations (MRF filter strength 0.07): 40s
AMAP peaks: [CSF,GM,WM] = [0.40±0.07,0.69±0.09,0.97±0.04]
Final cleanup (gcutstr=0.25):
Level 1 cleanup (ROI estimation) 4s
Level 1 cleanup (brain masking) 1s
Level 2 cleanup (CSF correction) 1s
Level 3 cleanup (CSF/WM PVE) 1s
8s
Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
Template: "C:\Work\Dev\Divers\spm12\toolbox\cat12\templates_volumes\Template_0_IXI555_MNI152_GS.nii"
1 | 2.50 | 0.0546 0.0000 0.0546
2 | 2.50 | 0.0547 0.0002 0.0548
3 | 2.50 | 0.0546 0.0002 0.0549
16 | 2.25 | 0.0462 0.0002 0.0464
17 | 2.25 | 0.0455 0.0007 0.0462
30 | 2.00 | 0.0439 0.0009 0.0448
31 | 2.00 | 0.0420 0.0013 0.0432
44 | 1.75 | 0.0404 0.0015 0.0419
45 | 1.75 | 0.0390 0.0018 0.0409
58 | 1.50 | 0.0367 0.0020 0.0387
59 | 1.50 | 0.0352 0.0024 0.0376
Shooting registration with 2.50:-0.25:1.50 mm takes: 117s
Prepare output 18s
135s
Jacobian determinant (RMS): 0.005 0.026 0.043 0.056 0.067 | 0.069682
Template Matching: 0.164 0.137 0.126 0.117 0.106 | 0.105606
Write result maps: 14s
Surface and thickness estimation:
lh:
Thickness estimation (0.50 mm³):
WM distance: 47s
CSF distance: 22s
PBT2x thickness: 14s
96s
Create initial surface 49s
Topology correction and surface refinement: 108s
Correction of central surface in highly folded areas 19s
Refine central surface 129s
Correction of central surface in highly folded areas 2 15s
Spherical mapping with areal smoothing 148s
Spherical registration 338s
Euler number / defect number / defect size: -50 / 25 / 1.29%
rh:
Thickness estimation (0.50 mm³):
WM distance: 51s
CSF distance: 22s
PBT2x thickness: 14s
100s
Create initial surface 50s
Topology correction and surface refinement: 113s
Correction of central surface in highly folded areas 12s
Refine central surface 126s
Correction of central surface in highly folded areas 2 15s
Spherical mapping with areal smoothing 148s
Spherical registration 333s
Euler number / defect number / defect size: -62 / 28 / 1.59%
cb:
Thickness estimation (0.50 mm³):
WM distance: 11s
CSF distance: 7s
PBT2x thickness: 5s
26s
Create initial surface 13s
Topology correction and surface refinement: 41s
Correction of central surface in highly folded areas 46s
Refine central surface 338s
Correction of central surface in highly folded areas 2 27s
Spherical mapping with areal smoothing 284s
Spherical registration 425s
Euler number / defect number / defect size: -426 / 52 / 8.84%
Final cerebral surface processing results:
Average thickness: 3.3823 ± 1.0296 mm
Surface intensity / position RMSE: 0.0670 / 0.0926
Euler number / defect number / defect size: 183.3 / 35.0 / 3.90%
Display thickness: C:\Users\franc\.brainstorm\tmp\cat12\surf\lh.thickness.CAT12_ICBM152
Display thickness: C:\Users\franc\.brainstorm\tmp\cat12\surf\rh.thickness.CAT12_ICBM152
Display thickness: C:\Users\franc\.brainstorm\tmp\cat12\surf\cb.thickness.CAT12_ICBM152
Surface ROI estimation: Surface and thickness estimation takes: 3119s
ROI estimation in native space:
0s
Quality check: 6s
Developer display mode!
Print 'Graphics' figure to:
C:\Users\franc\.brainstorm\tmp\cat12\report\catreport_CAT12_ICBM152.pdf
------------------------------------------------------------------------
CAT preprocessing takes 66 minute(s) and 12 second(s).
Image Quality Rating (IQR): 86.18% (B)
Segmentations are saved in C:\Users\franc\.brainstorm\tmp\cat12\mri
Reports are saved in C:\Users\franc\.brainstorm\tmp\cat12\report
Labels are saved in C:\Users\franc\.brainstorm\tmp\cat12\label
------------------------------------------------------------------------
Remove "C:\Users\franc\.brainstorm\tmp\cat12\label\catROI_CAT12_ICBM152.xml" from dependency list because it does not exist!
One or multiple files do not exist and were removed from the dependency list
and following batches will may not work correctly!
Remove "C:\Users\franc\.brainstorm\tmp\cat12\report\catlog_CAT12_ICBM152.txt" from dependency list because it does not exist!
One or multiple files do not exist and were removed from the dependency list
and following batches will may not work correctly!
10-Nov-2020 20:52:02 - Done 'CAT12: Segmentation (current release)'
10-Nov-2020 20:52:02 - Running 'Extract additional surface parameters'
1/1) Extract parameters for C:\Users\franc\.brainstorm\tmp\cat12\surf\lh.central.CAT12_ICBM152.gii
3s - Display C:\Users\franc\.brainstorm\tmp\cat12\surf\lh.gyrification.CAT12_ICBM152
22s - Display C:\Users\franc\.brainstorm\tmp\cat12\surf\lh.depth.CAT12_ICBM152
3s - Display C:\Users\franc\.brainstorm\tmp\cat12\surf\rh.gyrification.CAT12_ICBM152
23s - Display C:\Users\franc\.brainstorm\tmp\cat12\surf\rh.depth.CAT12_ICBM152
10-Nov-2020 20:52:53 - Done 'Extract additional surface parameters'
10-Nov-2020 20:52:53 - Done
If you look in the folder $HOME/.brainstorm/tmp/cat12 after the process is done, you will find the output of CAT. Make a copy of this folder if you think you might need to re-import the subject later.
This includes the quality control reports, in the report subfolder:
In Brainstorm, the surfaces, atlases and surface measures are imported correctly:
