Dear Sally,
that rather looks like an issue with file writing and I would simply try to preprocess these data again. Probably you have to remove the old preprocessing that were not successful.
Best,
Christian
On Thu, 27 May 2021 16:55:07 +0100, Sally Chester <[log in to unmask]> wrote:
>Hello CAT12/SPM experts!
>
>I am new to CAT12 (and this field in general!) and I am getting an error message when I try to segment 97 T1w scans. I am segmenting 97 scans in total, but for 12 random scans I get the error below (and in detail at the end of the message). I can see from the archives that this has been mentioned before (Thu, 29 Jun 2017 15:37:21 by Andreia N. Queirós) but I cannot see a solution.
>
>------------------------------------------------------------------------
>CAT Preprocessing error for sub-85_T1w:
>------------------------------------------------------------------------
>** not well-formed (invalid token) at line 75
>input_gifti: cannot read image
>Error in input file.
>
>------------------------------------------------------------------------
> 27 - cat_check_system_output
> 803 - cat_surf_createCS
> 699 - cat_main1639
> 949 - cat_run_job1639
> 34 - cat_run_newcatch
> 866 - run_job
> 455 - cat_run
> 29 - cfg_run_cm
> 1717 - local_runcj
> 972 - cfg_util
> 710 - MenuFileRun_Callback
> 95 - gui_mainfcn
> 53 - cfg_ui
>------------------------------------------------------------------------
>
>
>I find it odd as the majority of the time the process works all the way to the end, but on certain scans it throws an error.
>
>My hardware/software is as follows:
>macOS Big Sur version 11.3.1
>Matlab_R2020b
>SPM12 (with updates_r7771)
>latest CAT12 version
>(number of processes set to 0)
>
>Any help would be appreciated!
>
>Many thanks,
>Sally
>
>
>------------------------------------------------------------------------
>CAT12.7 r1743: 85/97: /Desktop/nifti_spgr/sub-85_T1w.nii
>------------------------------------------------------------------------
>SANLM denoising (medium): 69s
>APP: Rough bias correction:
> Initialize 6s
> Estimate background 4s
> Initial correction 8s
> Refine background 4s
> Final correction 7s
> Final scaling 10s
> 45s
>Affine registration 15s
>Affine registration 10s
>SPM preprocessing 1 (estimate 1): 77s
>SPM preprocessing 1 (estimate 2): 53s
>SPM preprocessing 2 (write):
> Write Segmentation 22s
> Update Segmentation 34s
> Update Skull-Stripping 33s
> Update probability maps 7s
> 97s
>Global intensity correction: 14s
>SANLM denoising after intensity normalization (medium): 15s
>Fast registration 30s
>Local adaptive segmentation (LASstr=0.50):
> Prepare maps 4s
> Prepare partitions 1s
> Prepare segments (LASmod = 1.09) 11s
> Estimate local tissue thresholds (WM) 16s
> Estimate local tissue thresholds (GM) 20s
> Estimate local tissue thresholds (CSF/BG) 4s
> Intensity transformation 60s
> SANLM denoising after LAS (medium) 35s
> 35s
>ROI segmentation (partitioning):
> Atlas -> subject space 7s
> Major structures 3s
> Ventricle detection 8s
> Blood vessel detection 8s
> WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 18s
> Manual stroke lesion detection 0s
> Closing of deep structures 1s
> Side alignment 3s
> Final corrections 3s
> 52s
>Blood vessel correction (BVCstr=0.50): 1s
>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 14s
> AMAP peaks: [CSF,GM,WM] = [0.42±0.06,0.69±0.08,0.97±0.04]
>Final cleanup (gcutstr=0.25):
> Level 1 cleanup (ROI estimation) 3s
> Level 1 cleanup (brain masking) 1s
> Level 2 cleanup (CSF correction) 1s
> Level 3 cleanup (CSF/WM PVE) 1s
> 6s
>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
> Template: "/Applications/spm12/toolbox/cat12/templates_volumes/Template_0_IXI555_MNI152_GS.nii"
> 1 | 2.50 | 0.0631 0.0000 0.0631
> 2 | 2.50 | 0.0618 0.0006 0.0624
> 3 | 2.50 | 0.0613 0.0009 0.0622
> 16 | 2.25 | 0.0618 0.0010 0.0628
> 17 | 2.25 | 0.0533 0.0023 0.0556
> 18 | 2.25 | 0.0515 0.0026 0.0542
> 30 | 2.00 | 0.0527 0.0052 0.0580
> 31 | 2.00 | 0.0487 0.0040 0.0526
> 32 | 2.00 | 0.0477 0.0044 0.0521
> 44 | 1.75 | 0.0476 0.0066 0.0543
> 45 | 1.75 | 0.0451 0.0055 0.0506
> 46 | 1.75 | 0.0445 0.0058 0.0503
> 58 | 1.50 | 0.0451 0.0077 0.0528
> 59 | 1.50 | 0.0416 0.0070 0.0485
> 60 | 1.50 | 0.0408 0.0074 0.0482
>Shooting registration with 2.50:-0.25:1.50 mm takes: 77s
> Prepare output 11s
> 88s
> Jacobian determinant (RMS): 0.104884
> Template Matching: 0.122414
>Write result maps: 1s
>Surface and thickness estimation:
>lh:
> Thickness estimation (0.50 mm³):
> WM distance: 18s
> CSF distance: 8s
> PBT2x thickness: 6s
> 35s
> Create initial surface 44s
> Topology correction and surface refinement: 64s
> Correction of central surface in highly folded areas
>------------------------------------------------------------------------
>CAT Preprocessing error for sub-85_T1w:
>------------------------------------------------------------------------
>** not well-formed (invalid token) at line 75
>input_gifti: cannot read image
>Error in input file.
>
>------------------------------------------------------------------------
> 27 - cat_check_system_output
> 803 - cat_surf_createCS
> 699 - cat_main1639
> 949 - cat_run_job1639
> 34 - cat_run_newcatch
> 866 - run_job
> 455 - cat_run
> 29 - cfg_run_cm
> 1717 - local_runcj
> 972 - cfg_util
> 710 - MenuFileRun_Callback
> 95 - gui_mainfcn
> 53 - cfg_ui
>------------------------------------------------------------------------
>
>Print 'Graphics' figure to:
> /Desktop/nifti_spgr/report/catreport_sub-85_T1w.pdf
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