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Dear Andreia, for extracting ROI-values for SBM you can use the functions: CAT12 -> Extract ROI Data -> Extract ROI-based Surface values and then CAT12 -> Extract ROI Data -> Estimate Mean values inside ROI for external analysis Best, Christian On Fri, 7 Jul 2017 16:15:26 +0100, Andreia N. Queirós <[log in to unmask]> wrote: >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 > >============================================================================================= > >To get started, type one of these: helpwin, helpdesk, or demo. >For product information, visit www.mathworks.com. > >CAT parallel processing with MATLAB PID: 7384 > >------------------------------------------------------------------------ >CAT12 r1152: 1/1: .\Nifti\sB003036-0016-00001-000176-01.nii >------------------------------------------------------------------------ >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)] > >------------------------------------------------------------------------ >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.