Dear Doctor Gaser,
Thank you so much for your help and sorry for the delayed response.
We tried your latest suggestions but with no success. However, as we mentioned in our previous post, we have since switched to a computer with a greater RAM memory and it solved our issues.
We stumbled upon a new issue and we would be very grateful if you could help us once again:
We are trying to extract VBM and SBM values for regions such as the Insula. we intend to analyze these values with SPSS so that we can test for associations with self-reported measures.
We were successful with VBM but don't understand the step-by-step procedure to do the same with SBM. Could you be so kind as to guide in this process?
Furthermore, as requested, please find below the full output from the pc that caused the trouble.
Thank you so much for your time and consideration.
Best regards,
Andreia N. Queirós
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CAT parallel processing with MATLAB PID: 7384
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CAT12 r1152: 1/1: .\Nifti\sB003036-0016-00001-000176-01.nii
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APP: Rough bias correction:
Initialize 36s
Estimate background 3s
Initial correction 37s
Refine background 4s
Final correction 6s
Background correction 1s
Final scaling 4s
92s
Coarse affine registration 9s
Affine registration 11s
SPM preprocessing 1 (estimate): 108s
SPM preprocessing 2 (write): 119s
Global intensity correction: 21s
SANLM noise correction: 42s
Local adaptive segmentation (LASstr=0.50):
Prepare maps 6s
Prepare partitions 3s
Prepare segments (LASmod = 1.13) 26s
Estimate local tissue thresholds 71s
SANLM noise correction for LAS 20s
126s
ROI segmentation (partitioning):
Atlas -> subject space 26s
Major structures 9s
Ventricle detection 16s
Blood vessel detection 6s
WMH detection (WMHCstr=0.50) 19s
Closing of deep structures 2s
Side alignment 8s
Final corrections 3s
89s
Blood vessel correction (BVCstr=0.50): 2s
Skull-stripping using graph-cut (gcutstr=0.50):
WM initialisation 6s
GM region growing 3s
GM-CSF region growing 7s
CSF region growing 7s
Ventricle filling 4s
28s
Amap using initial SPM12 segmentations (MRF filter strength 0.06): 56s
AMAP peaks: [CSF,GM,WM] = [0.38±0.08,0.69±0.09,0.98±0.04]
Final cleanup (gcutstr=0.50):
Level 1 cleanup (ROI estimation) 6s
Level 1 cleanup (brain masking) 4s
Level 2 cleanup (CSF correction) 3s
Level 3 cleanup (CSF/WM PVE) 3s
16s
Internal WMH correction for spatial normalization (WMHCstr=0.50): 4s
Dartel registration with 1.50 mm:
1 | 0.2362 | 501522 0 501522 430.118
2 | 0.1826 | 387676 31974 419649 200.953
3 | 0.1812 | 384672 28787 413459 51.053
4 | 0.1815 | 385417 15046 400464 197.762
5 | 0.1665 | 353491 36139 389630 68.090
6 | 0.1669 | 354277 34510 388787 42.982
7 | 0.1685 | 357754 17953 375707 170.195
8 | 0.1529 | 324679 39356 364035 63.612
9 | 0.1530 | 324721 38131 362852 37.846
10 | 0.1538 | 326477 19999 346476 148.656
11 | 0.1380 | 293043 41020 334062 61.293
12 | 0.1373 | 291548 40739 332288 38.299
13 | 0.1376 | 292217 21533 313750 121.292
14 | 0.1243 | 263928 38575 302502 55.106
15 | 0.1229 | 260869 39679 300548 36.356
16 | 0.1221 | 259306 41781 301088 42.305
17 | 0.1216 | 258153 41948 300101 30.597
18 | 0.1211 | 257014 42856 299869 27.945
256s
Write result maps: 34s
Surface and thickness estimation:
lh:
Thickness estimation (0.50 mm³):
WM distance: 85s
CSF distance: 66s
PBT2x thickness: 63s
Final Corrections: 229s
Create initial surface
Setting up...
Starting main process...
Done with 10 percent.
Done with 20 percent.
Done with 30 percent.
Done with 40 percent.
Done with 50 percent.
Done with 60 percent.
Done with 70 percent.
Done with 80 percent.
Done with 90 percent.
Done with 100 percent.
Made 54 adjustments.
Extracting component with largest number of vertices...
Vertices: 705238 Triangles: 1410492
Setting up...
Starting main process...
Done with 10 percent.
Done with 20 percent.
Done with 30 percent.
Done with 40 percent.
Done with 50 percent.
Done with 60 percent.
Done with 70 percent.
Done with 80 percent.
Done with 90 percent.
Done with 100 percent.
Made 1 adjustments.
Extracting component with largest number of vertices...
Vertices: 705170 Triangles: 1410360
26s
Reduce surface to 100000 faces: Resampled into 286268 polygons.
Extract largest of 129 components.
70s
Topology correction and surface refinement [Warning: Control Character '\P' is not valid. See 'doc sprintf' for control characters valid in the format string.]
[> In cat_io_cprintf (line 156)
In cat_run_newcatch (line 36)
In cat_run>run_job (line 276)
In cat_run (line 155)]
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CAT Preprocessing error: CAT:system_error: . 27 - cat_check_system_output
422 - cat_surf_createCS
1644 - cat_main
633 - cat_run_job1070
14 - cat_run_newcatch
276 - run_job
155 - cat_run
------------------------------------------------------------------------
Error:cat_io_report:CATgui: Error in cat_io_report GUI parameter report creation > incomple CAT parameters.
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