CORR_cat12.8.1/IPCAS_1/sub-0025511/ses-1/report/cat_sub-0025511_ses-1_run-1_T1w.xml

<?xml version="1.0" encoding="utf-8"?>
<S>
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      <path>/var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1</path>
      <file>sub-0025511_ses-1_run-1_T1w</file>
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      <fnames>..IPCAS_1/sub-0025511/ses-1/sub-0025511_ses-1_run-1_T1w</fnames>
   </filedata>
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         <biasfwhm>60</biasfwhm>
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      </opts>
      <extopts>
         <uhrlim>1.4</uhrlim>
         <gcutstr>2</gcutstr>
         <cleanupstr>0.5</cleanupstr>
         <spm_kamap>0</spm_kamap>
         <NCstr>-Inf</NCstr>
         <LASstr>0.5</LASstr>
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         <WMHC>2</WMHC>
         <WMHCstr>0.5</WMHCstr>
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         <restype>optimal</restype>
         <resval>[1 0.3]</resval>
         <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
         <bids_yes>0</bids_yes>
         <nproc>1</nproc>
         <species>human</species>
         <APP>1070</APP>
         <setCOM>1</setCOM>
         <vox>1.5</vox>
         <bb>12</bb>
         <shootingsurf>Template_T1</shootingsurf>
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         <darteltpm>
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         <shootingT1>
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         </shootingT1>
         <brainmask>
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         </brainmask>
         <T1>
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         </T1>
         <cat12atlas>
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         <pbtres>0.5</pbtres>
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         <verb>2</verb>
         <ignoreErrors>1</ignoreErrors>
         <expertgui>1</expertgui>
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         <experimental>0</experimental>
         <print>2</print>
         <fontsize>10</fontsize>
         <send_info>1</send_info>
         <gifti_dat>1</gifti_dat>
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                  <item>wm</item>
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            <tr>
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            <tr>
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            <tr>
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               <td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
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               <td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
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            <tr>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
               <td>1</td>
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            <tr>
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            <tr>
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            <tr>
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               <td>0</td>
               <td>1</td>
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            <tr>
               <td>Destrieux</td>
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               <td>0</td>
               <td>1</td>
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            <tr>
               <td>HCP</td>
               <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
               <td>0</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_100P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_200P_17N</td>
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               <td>0</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_400P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <tr>
               <td>Schaefer2018_600P_17N</td>
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               <td>1</td>
               <td>0</td>
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            <VT>15</VT>
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            <HD>21</HD>
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            <PH>25</PH>
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      <SurfaceDefectArea>1.12155017259608</SurfaceDefectArea>
      <SurfaceDefectNumber>1.6</SurfaceDefectNumber>
      <SurfaceIntensityRMSE>1.34020268917084</SurfaceIntensityRMSE>
      <SurfacePositionRMSE>1.43578910827637</SurfacePositionRMSE>
      <SIQR>2.74889716271638</SIQR>
      <IQR>2.42919718493452</IQR>
   </qualityratings>
   <ratings_help>
      <qualitymeasures>
         <res_vx_vol>voxel dimensions</res_vx_vol>
         <res_RMS>RMS error of voxel size</res_RMS>
         <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
         <res_BB>brain next to the image boundary</res_BB>
         <tissue_mn>mean within the tissue classes</tissue_mn>
         <tissue_std>standard deviation within the tissue classes</tissue_std>
         <contrast>contrast between tissue classes</contrast>
         <contrastr>contrast between tissue classes</contrastr>
         <NCR>noise to contrast ratio</NCR>
         <ICR>inhomogeneity to contrast ratio</ICR>
         <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
         <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
         <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
         <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
      </qualitymeasures>
      <subjectmeasures>
         <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
         <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
         <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
         <surf_TSA>total surface area</surf_TSA>
      </subjectmeasures>
   </ratings_help>
   <software>
      <version_segment>1639</version_segment>
      <system>LINUX</system>
      <version_spm>7771</version_spm>
      <version_matlab>9.3</version_matlab>
      <version_cat>12.8.1</version_cat>
      <revision_cat>2040</revision_cat>
      <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
      <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
      <qamethod>cat12</qamethod>
      <date>20231031-010718</date>
   </software>
   <subjectmeasures>
      <software>
         <version_segment>1639</version_segment>
      </software>
      <qualitymeasures>
         <software>
            <version_segment>1639</version_segment>
         </software>
         <SurfaceEulerNumber>16</SurfaceEulerNumber>
         <SurfaceDefectArea>0.48620069038434</SurfaceDefectArea>
         <SurfaceDefectNumber>12</SurfaceDefectNumber>
         <SurfaceIntensityRMSE>0.0670101344585419</SurfaceIntensityRMSE>
         <SurfacePositionRMSE>0.0717894583940506</SurfacePositionRMSE>
      </qualitymeasures>
      <EC_abs>16</EC_abs>
      <defect_size>0.48620069038434</defect_size>
      <vol_abs_CGW>[247.758960784314 719.226074509804 475.962282352941 0 0]</vol_abs_CGW>
      <vol_abs_WMH>0.146352941176471</vol_abs_WMH>
      <vol_rel_WMH>0.000101426392624729</vol_rel_WMH>
      <surf_TSA>1990.57420103438</surf_TSA>
      <vol_TIV>1442.94731764706</vol_TIV>
      <vol_rel_CGW>[0.171703400224148 0.498442365645483 0.329854234130369 0 0]</vol_rel_CGW>
      <dist_thickness>
         <item>[2.48997447090498 0.598957691551069]</item>
      </dist_thickness>
      <dist_thickness_kmeans>[2.47889351844788 0.68159900292489 1]</dist_thickness_kmeans>
      <dist_thickness_kmeans_inner3>[1.92790363302739 0.222430664514215 0.302976438342542;2.51021896230781 0.168049871716808 0.43054252099169;3.14178267423977 0.249604918487973 0.266481040665768]</dist_thickness_kmeans_inner3>
      <dist_thickness_kmeans_outer2>[0.925588677164929 0.344171913819393 0.518714260959972;4.00335499937743 0.301996646856481 0.481285739040028]</dist_thickness_kmeans_outer2>
   </subjectmeasures>
   <subjectratings>
      <vol_TIV>1.04381814295531</vol_TIV>
      <vol_rel_CGW>[0.93360991781875 6.80176662438008 3.77396253826094 0.5 0.5]</vol_rel_CGW>
      <vol_rel_WMH>1.01014263926247</vol_rel_WMH>
      <surf_TSA>8.62105585417206</surf_TSA>
      <SQR>5.56847081791823</SQR>
   </subjectratings>
   <ppe>
      <affreg>
         <skullstrippedpara>[0 1 0 11156.849 0.420866942567438]</skullstrippedpara>
         <skullstripped>[false]</skullstripped>
         <highBGpara>[0.00194592075422406 0.00174089067149907 0.0111741609871387]</highBGpara>
         <highBG>[false]</highBG>
      </affreg>
      <SPMvols0>[847.902980392157 413.746694117647 550.459176470588 1065.59227843137 1001.1537372549 7908.30097254902]</SPMvols0>
      <SPMvols1>[722.458470588235 388.195156862745 300.653129411765 519.082968627451 800.90542745098 8409.99392156863]</SPMvols1>
      <tths>
         <gintnorm>
            <T3th>[60.5085983276367 202.926406860352 323.498992919922]</T3th>
            <Tth>
               <T3th>[-69.2560195922852 -50.9229125976562 1.80499815940857 60.5085983276367 202.926406860352 323.498992919922 454.994201660156 970.884338378906]</T3th>
               <T3thx>[0 0.02 0.05 1 2 3 4 5]</T3thx>
            </Tth>
         </gintnorm>
      </tths>
      <reginitp>
         <opt>
            <nits>16</nits>
            <vxreg>1.5</vxreg>
            <rres>3</rres>
            <stepsize>0.5</stepsize>
            <resfac>[1 1 1 1 1]</resfac>
            <ll1th>0.015</ll1th>
            <ll3th>[0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03;0.03 0.03 0.03 0.03 0.03]</ll3th>
            <regstr>15</regstr>
         </opt>
         <fast>0</fast>
         <clsn>2</clsn>
         <regra>1</regra>
         <testfolder>Shooting_Template_0_GS_tr1.5_rr3.0-3.0_or1.5_regstr15.0</testfolder>
         <dtc>[0.0197392012923956 0.0742368027567863 0.0828839093446732 0 0]</dtc>
         <ll>[0.0845981458989846 0 0.0845981458989846 0;0.204529211586979 0.0105186178475296 0.215047829434508 2243.07421875;0.204529211586979 0.0105186178475296 0.215047829434508 2243.07421875]</ll>
         <rmsdtc>[0.0444976724684238 0.102725222706795 0.11591163277626]</rmsdtc>
         <rmsgdt>[0.0320467799901962 0.0492933951318264 0.0615515671670437]</rmsgdt>
         <rmsdt>0.11591163277626</rmsdt>
         <dt>0.0828839093446732</dt>
      </reginitp>
      <reg>
         <opt>
            <nits>64</nits>
            <vxreg>1.5</vxreg>
            <rres>1.5</rres>
            <stepsize>0.25</stepsize>
            <resfac>[1.66666666666667 1.5 1.33333333333333 1.16666666666667 1]</resfac>
            <ll1th>0.051</ll1th>
            <ll3th>[0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501;0.0501 0.0501 0.0501 0.0501 0.0501]</ll3th>
            <regstr>0.5</regstr>
         </opt>
         <fast>0</fast>
         <clsn>2</clsn>
         <regra>1</regra>
         <testfolder>Shooting_Template_0_GS_tr1.5_rr2.5-1.5_or1.5_regstr0.5</testfolder>
         <dtc>[0.00817362125962973 0.0299821402877569 0.0436817780137062 0.0529331602156162 0.0604513101279736 0.0679881423711777]</dtc>
         <ll>[0.0821145328485892 0 0.0821145328485892 0;0.222003434065934 0.011303377785409 0.233306811851343 5785.91650390625;0.205052376853519 0.015331188085043 0.220383564938562 11034.0400390625;0.185378390726088 0.0185939230923413 0.203972313818429 20049.306640625;0.167946574390646 0.0224011570277697 0.190347731418416 39187.53125;0.167946574390646 0.0224011570277697 0.190347731418416 39187.53125]</ll>
         <rmsdtc>[0.00990081671625376 0.0365082025527954 0.0566487871110439 0.0835081487894058 0.109725326299667 0.11741366237402]</rmsdtc>
         <rmsgdt>[0.00306661170907319 0.0124246887862682 0.0283955577760935 0.0509931892156601 0.0712620690464973 0.0771862491965294]</rmsgdt>
         <rmsdt>0.11741366237402</rmsdt>
         <dt>0.0679881423711777</dt>
      </reg>
   </ppe>
   <catlog>
      <item>------------------------------------------------------------------------</item>
      <item>CAT12.8.1 r2040: 1/1: ./sub-0025511/ses-1/sub-0025511_ses-1_run-1_T1w.n</item>
      <item>------------------------------------------------------------------------</item>
      <item>SANLM denoising (medium): 34s</item>
      <item>Internal resampling (1.33x1.00x1.00mm &gt; 1.00x1.00x1.00mm): 1s</item>
      <item>APP: Rough bias correction:</item>
      <item>Initialize 6s</item>
      <item>Estimate background 5s</item>
      <item>Initial correction 5s</item>
      <item>Refine background 3s</item>
      <item>Final correction 4s</item>
      <item>Final scaling 4s</item>
      <item>34s</item>
      <item>Correct center-of-mass 3s</item>
      <item>Affine registration 8s</item>
      <item>SPM preprocessing 1 (estimate 1 - TPM registration): 67s</item>
      <item>SPM preprocessing 1 (estimate 2): 64s</item>
      <item>SPM preprocessing 2 (write):</item>
      <item>Write Segmentation 16s</item>
      <item>Update Segmentation 18s</item>
      <item>Update Skull-Stripping 41s</item>
      <item>Update probability maps 8s</item>
      <item>83s</item>
      <item>Global intensity correction: 16s</item>
      <item>SANLM denoising after intensity normalization (medium): 25s</item>
      <item>Fast Optimized Shooting registration 31s</item>
      <item>Local adaptive segmentation (LASstr=0.50):</item>
      <item>Prepare maps 4s</item>
      <item>Prepare partitions 2s</item>
      <item>Prepare segments (LASmod = 1.00) 13s</item>
      <item>Estimate local tissue thresholds (WM) 18s</item>
      <item>Estimate local tissue thresholds (GM) 28s</item>
      <item>Intensity transformation 0s</item>
      <item>SANLM denoising after LAS (medium) 37s</item>
      <item>106s</item>
      <item>ROI segmentation (partitioning):</item>
      <item>Atlas -&gt; subject space 7s</item>
      <item>Major structures 3s</item>
      <item>Ventricle detection 17s</item>
      <item>Blood vessel detection 9s</item>
      <item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.08) 22s</item>
      <item>Manual stroke lesion detection 0s</item>
      <item>Closing of deep structures 2s</item>
      <item>Side alignment 3s</item>
      <item>Final corrections 4s</item>
      <item>68s</item>
      <item>Blood vessel correction (BVCstr=0.50): 2s</item>
      <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s</item>
      <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 0.05]</item>
      <item>Final cleanup (gcutstr=0.25):</item>
      <item>Level 1 cleanup (ROI estimation) 4s</item>
      <item>Level 1 cleanup (brain masking) 3s</item>
      <item>Level 2 cleanup (CSF correction) 1s</item>
      <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
      <item>11s</item>
      <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
      <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
      <item>1 | 2.50 | 0.0821 0.0000 0.0821 | 32.0000</item>
      <item>2 | 2.50 | 0.0803 0.0009 0.0812 | 29.4886</item>
      <item>3 | 2.50 | 0.0797 0.0014 0.0811 | 26.9772</item>
      <item>4 | 2.50 | 0.0794 0.0016 0.0810 | 24.6107</item>
      <item>5 | 2.50 | 0.0792 0.0017 0.0809 | 22.6548</item>
      <item>6 | 2.50 | 0.0790 0.0018 0.0808 | 20.6989</item>
      <item>7 | 2.50 | 0.0788 0.0019 0.0807 | 18.9688</item>
      <item>8 | 2.50 | 0.0786 0.0020 0.0805 | 17.4455</item>
      <item>9 | 2.50 | 0.0783 0.0020 0.0804 | 15.9223</item>
      <item>10 | 2.50 | 0.0781 0.0021 0.0802 | 14.6627</item>
      <item>11 | 2.50 | 0.0778 0.0022 0.0800 | 13.4764</item>
      <item>12 | 2.50 | 0.0776 0.0022 0.0798 | 12.3015</item>
      <item>13 | 2.50 | 0.0773 0.0023 0.0797 | 11.3776</item>
      <item>14 | 2.50 | 0.0771 0.0024 0.0795 | 10.4537</item>
      <item>15 | 2.25 | 0.0765 0.0025 0.0790 | 9.5920</item>
      <item>16 | 2.25 | 0.0740 0.0038 0.0778 | 8.8725</item>
      <item>29 | 2.00 | 0.0761 0.0017 0.0778 | 3.3283</item>
      <item>30 | 2.00 | 0.0703 0.0041 0.0744 | 3.1221</item>
      <item>31 | 2.00 | 0.0684 0.0051 0.0735 | 2.9160</item>
      <item>43 | 1.75 | 0.0678 0.0029 0.0707 | 1.5785</item>
      <item>44 | 1.75 | 0.0633 0.0053 0.0686 | 1.5194</item>
      <item>45 | 1.75 | 0.0618 0.0062 0.0680 | 1.4626</item>
      <item>57 | 1.50 | 0.0606 0.0045 0.0651 | 1.0900</item>
      <item>58 | 1.50 | 0.0571 0.0067 0.0639 | 1.0730</item>
      <item>59 | 1.50 | 0.0560 0.0075 0.0634 | 1.0579</item>
      <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 165s</item>
      <item>Prepare output 10s</item>
      <item>175s</item>
      <item>Jacobian determinant (RMS): 0.010 0.037 0.057 0.084 0.110 | 0.117414</item>
      <item>Template Matching: 0.082 0.222 0.205 0.185 0.168 | 0.167947</item>
      <item>Write result maps: 54s</item>
      <item>Surface and thickness estimation:</item>
      <item>lh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 34s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 45s</item>
      <item>101s</item>
      <item>Create initial surface 85s</item>
      <item>Topology correction: 102s</item>
      <item>Surface refinement: 86s</item>
      <item>Reduction of surface collisions with optimization: 73s</item>
      <item>Spherical mapping with areal smoothing 81s</item>
      <item>Spherical registration 291s</item>
      <item>rh:</item>
      <item>Thickness estimation (0.50 mm ):</item>
      <item>WM distance: 28s</item>
      <item>CSF distance: 15s</item>
      <item>PBT2x thickness: 43s</item>
      <item>90s</item>
      <item>Create initial surface 80s</item>
      <item>Topology correction: 93s</item>
      <item>Surface refinement: 79s</item>
      <item>Reduction of surface collisions with optimization: 72s</item>
      <item>Spherical mapping with areal smoothing 81s</item>
      <item>Spherical registration 311s</item>
      <item>Final surface processing results:</item>
      <item>Average thickness (FS): 2.4900 0.5984 mm</item>
      <item>Surface intensity / position RMSE: 0.0670 / 0.0718</item>
      <item>Euler number / defect number / defect size: 16.0 / 12.0 / 0.49%</item>
      <item>Display thickness: /var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1/surf/lh.thickness.sub-0025511_ses-1_run-1_T1w</item>
      <item>Display thickness: /var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1/surf/rh.thickness.sub-0025511_ses-1_run-1_T1w</item>
      <item>Show surfaces in orthview: /var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1/sub-0025511_ses-1_run-1_T1w.nii</item>
      <item>Surface ROI estimation: 9s</item>
      <item>Surface and thickness estimation takes: 1722s</item>
      <item>ROI estimation in native space:</item>
      <item>ROI estimation of 'cobra' atlas 7s</item>
      <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
      <item>ROI estimation of 'lpba40' atlas 8s</item>
      <item>ROI estimation of 'hammers' atlas 19s</item>
      <item>ROI estimation of 'thalamus' atlas 2s</item>
      <item>ROI estimation of 'ibsr' atlas 7s</item>
      <item>ROI estimation of 'aal3' atlas 11s</item>
      <item>ROI estimation of 'mori' atlas 17s</item>
      <item>ROI estimation of 'anatomy3' atlas 24s</item>
      <item>ROI estimation of 'julichbrain' atlas 32s</item>
      <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
      <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
      <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 57s</item>
      <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s</item>
      <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
      <item>Write results 9s</item>
      <item>343s</item>
      <item>Quality check: 11s</item>
      <item>Print 'Graphics' figure to:</item>
      <item>/var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1/report/catreport_sub-0025511_ses-1_run-1_T1w.pdf</item>
      <item>------------------------------------------------------------------------</item>
      <item>CAT preprocessing takes 49 minute(s) and 26 second(s).</item>
      <item>Image Quality Rating (IQR): 80.71% (B-)</item>
      <item>GM volume (GMV): 49.84% (719.23 / 1442.95 ml)</item>
      <item>GM thickness (GMT): 2.49 0.60 mm</item>
      <item>Segmentations are saved in /var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1/mri</item>
      <item>Reports are saved in /var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1/report</item>
      <item>Labels are saved in /var/lib/condor/execute/dir_613893/ds/IPCAS_1/sub-0025511/ses-1/label</item>
      <item>------------------------------------------------------------------------</item>
   </catlog>
</S>