Dear Bruno,
please try a newer CAT12 version, your version is 2.5 years old. This seems to be an older issue on windows systems.
Best,
Christian
On Tue, 11 Feb 2020 10:50:41 +0000, Bruno Robalo <[log in to unmask]> wrote:
>Dr. Gaser and all,
>
>I am having the same problem previously reported in 2016 by Dr. Jaime Shinsuke Ide (see link below) when I try to perform "Surface and thickness estimation" in CAT12. Re: CAT12 r938: Problems with read_gifti_file (Segmentation) - Wed, 1 Jun 2016 18:21:23 -0400
>
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;7a2e1c65.1606
>
>
>The problem happens during Thickness / Depth mapping when it tries to load the file "lh.central.*.gii" within the function "read_gifti_file". (see below the full error report)
>
>From what I understood from the message exchanges there was no apparent solution for the problem. Dr. Jaime Shinsuke Ide was running the segmentation on Windows when he had the error but as when he did the same on a Mac, the error did no happen anymore. unfortunately I don't have the possibility to switch operating systems to see if the problem still persists. I would like to know if anyone had the same problem and if there is any other workaround.
>
>I am working on a:
> - Windows 7
> - Matlab R2018a
> - SPM12: v6225
> - CAT12 r1207
>
>Thank you in advance for any help,
>
>Best,
>Bruno Robalo
>
>
>Error report:
>
>
>
>To get started, type one of these: helpwin, helpdesk, or demo.
>For product information, visit www.mathworks.com.
>
>CAT parallel processing with MATLAB PID: 2316
>
>------------------------------------------------------------------------
>CAT12 r1207: 1/1: X:\Bruno\DATA\HCP\teste\103818_T1.nii
>------------------------------------------------------------------------
>SANLM denoising (NCstr=Inf): 10s
>APP: Rough bias correction:
> Initialize 2s
> Estimate background 1s
> Initial correction 3s
> Refine background 2s
> Final correction 3s
> Background correction 0s
> Final scaling 1s
> 12s
>Coarse affine registration 8s
>Affine registration 5s
>SPM preprocessing 1 (estimate): 139s
>SPM preprocessing 2 (write): 31s
>Global intensity correction: 6s
>SANLM noise correction: 2s
>Local adaptive segmentation (LASstr=0.50):
> Prepare maps 2s
> Prepare partitions 0s
> Prepare segments (LASmod = 1.00) 6s
> Estimate local tissue thresholds 26s
> SANLM noise correction for LAS 2s
> 37s
>ROI segmentation (partitioning):
> Atlas -> subject space 3s
> Major structures 2s
> Ventricle detection 3s
> WMH detection (WMHCstr=0.50) 5s
> Closing of deep structures 1s
> Side alignment 2s
> Final corrections 1s
> 16s
>Skull-stripping using graph-cut (gcutstr=0.50):
> WM initialisation 2s
> GM region growing 1s
> GM-CSF region growing 2s
> CSF region growing 2s
> Ventricle filling 1s
> 7s
>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 12s
> AMAP peaks: [CSF,GM,WM] = [0.37±0.09,0.68±0.09,0.99±0.03]
>Final cleanup (gcutstr=0.40):
> Level 1 cleanup (ROI estimation) 2s
> Level 1 cleanup (brain masking) 1s
> Level 2 cleanup (CSF correction) 0s
> Level 3 cleanup (CSF/WM PVE) 1s
> 3s
>Permanent WMH correction (WMHCstr=0.50): 1s
>
>
>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
> Template: "X:\SPM_Naomi\spm12\toolbox\cat12\templates_1.50mm\Template_0_IXI555_MNI152_GS.nii"
> 1 | 2.50 | 0.0841 0.0000 0.0841 0.2682
> 2 | 2.50 | 0.0698 0.0366 0.1064 3.4462
> 3 | 2.50 | 0.0634 0.0053 0.0687 0.4519
> 4 | 2.50 | 0.0575 0.0054 0.0630 0.1078
> 5 | 2.50 | 0.0526 0.0059 0.0585 0.0790
> 6 | 2.50 | 0.0487 0.0061 0.0548 0.0661
> 7 | 2.50 | 0.0456 0.0061 0.0517 0.0520
> 8 | 2.50 | 0.0438 0.0060 0.0498 0.0383
> 9 | 2.50 | 0.0427 0.0059 0.0486 0.0277
> 10 | 2.50 | 0.0419 0.0059 0.0478 0.0191
> 11 | 2.50 | 0.0415 0.0058 0.0473 0.0129
> 12 | 2.50 | 0.0412 0.0058 0.0471 0.0085
> 16 | 2.25 | 0.0387 0.0237 0.0624 0.7575
> 17 | 2.25 | 0.0367 0.0070 0.0437 0.1579
> 18 | 2.25 | 0.0362 0.0065 0.0428 0.0397
> 30 | 2.00 | 0.0369 0.0241 0.0610 0.7446
> 31 | 2.00 | 0.0351 0.0078 0.0429 0.1567
> 44 | 1.75 | 0.0346 0.0201 0.0547 0.5099
> 45 | 1.75 | 0.0330 0.0085 0.0415 0.1155
> 58 | 1.50 | 0.0334 0.0204 0.0538 0.5249
> 59 | 1.50 | 0.0307 0.0097 0.0404 0.1488
> 60 | 1.50 | 0.0300 0.0095 0.0396 0.0725
>Shooting registration with 2.50:-0.25:1.50 mm takes: 167s
> Prepare output 12s
> 179s
> Jacobian determinant (RMS): 0.091 0.149 0.146 0.145 0.147 | 0.148436
> Template Matching: 0.124 0.109 0.105 0.099 0.090 | 0.090091
>Write result maps: 31s
>Surface and thickness estimation:
>lh:
> Thickness estimation (0.50 mm³):
> WM distance: 38s
> CSF distance: 36s
> PBT2x thickness: 19s
> Final Corrections: 102s
> 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 577 adjustments.
>Extracting component with largest number of vertices...
>Vertices: 508120 Triangles: 1016236
>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 275 adjustments.
>Extracting component with largest number of vertices...
>Vertices: 508088 Triangles: 1016172
> 13s
> Reduce surface to 100000 faces: Resampled into 200620 polygons.
>Extract largest of 14 components.
> 18s
> Topology correction and surface refinement find_selfintersections: .......................................................
>0 topological defects
>4 self intersection(s) to repair
>Post-patch: 1 self intersection(s) remaining
>Resampled into 142556 polygons.
>
>Resampled into 214512 polygons.
>
> 77s
> Spherical mapping with areal smoothing 143s
> Spherical registration 438s
> Thickness / Depth mapping [Warning: Escaped character '\B' is not valid. See 'doc sprintf' for supported special characters.]
>[> In cat_io_cprintf (line 156)
> In cat_run_newcatch (line 38)
> In cat_run>run_job (line 366)
> In cat_run (line 155)]
>
>------------------------------------------------------------------------
>CAT Preprocessing error for 103818_T1:
>------------------------------------------------------------------------
>[GIFTI] Loading of XML file X: 17 - read_gifti_file
> 71 - gifti
> 546 - cat_surf_createCS
> 1620 - cat_main
> 633 - cat_run_job1070
> 16 - cat_run_newcatch
> 366 - run_job
> 155 - cat_run
>------------------------------------------------------------------------
>
>{Error using read_gifti_file (line 17)
>[GIFTI] Loading of XML file X:\Bruno\DATA\HCP\teste\surf\lh.central.103818_T1.gii failed.
>
>Error in gifti (line 71)
> this = read_gifti_file(varargin{1},giftistruct);
>
>Error in cat_surf_createCS (line 546)
> CS = gifti(Pcentral);
>
>Error in cat_main (line 1620)
> [Yth1,S,Psurf] = cat_surf_createCS(VT,Ymix,Yl1,YMF,...
>
>Error in cat_run_job1070 (line 633)
> cat_main(res,obj.tpm,job);
>
>Error in cat_run_newcatch (line 16)
> cat_run_job1070(job,tpm,subj);
>
>Error in cat_run>run_job (line 366)
> cat_run_newcatch(job,tpm,subj);
>
>Error in cat_run (line 155)
>varargout{1} = run_job(job);
>
>Caused by:
> [GIFTI] Loading of XML file X:\Bruno\DATA\HCP\teste\surf\lh.central.103818_T1.gii failed.
>}
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