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- <Fm>/var/lib/condor/execute/dir_42422/ds/sub-0101/mri/msub-0101_ses-01_T1w.nii</Fm>
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- <fnames>..422/ds/sub-0101/sub-0101_ses-01_T1w</fnames>
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- <parameter>
- <opts>
- <tpm>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>64</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
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- </darteltpm>
- <shootingtpm>
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- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
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- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <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>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
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- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
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- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
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- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- </shootingtpms>
- <templates>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>62</SurfaceEulerNumber>
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- <res_vx_voli>[0.9375 0.899993896484375 0.9375]</res_vx_voli>
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- <res_BB>0</res_BB>
- <tissue_mn>[2.4449999332428 14.2019109725952 30.7090301513672 52.3710975646973]</tissue_mn>
- <tissue_mnr>[0.046686053276062 0.271178394556046 0.586373627185822 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[1.86700640105301 8.25215682835187 6.61322628054893 4.42011623454433]</tissue_std>
- <tissue_stdr>[0.0373953990638256 0.165287435054779 0.132460311055183 0.0885331779718399]</tissue_stdr>
- <contrast>18.1495609283447</contrast>
- <contrastr>0.346556812524796</contrastr>
- <NCR>0.162753149867058</NCR>
- <ICR>0.517574608325958</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.875 1.79998779296875 1.875]</res_vx_vol>
- <res_RMS>1.85033384869114</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.57347202301025 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.88498115539551</contrastr>
- <NCR>2.66742968559265</NCR>
- <ICR>1.74348866939545</ICR>
- <SurfaceEulerNumber>4.06122448979592</SurfaceEulerNumber>
- <SurfaceDefectArea>1.43959323692944</SurfaceDefectArea>
- <SurfaceDefectNumber>3.05</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.61336874961853</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.76177263259888</SurfacePositionRMSE>
- <IQR>2.46206370939333</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>1980</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>20220709-203205</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>62</SurfaceEulerNumber>
- <SurfaceDefectArea>1.75837294771776</SurfaceDefectArea>
- <SurfaceDefectNumber>41</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0806684419512749</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0880886316299438</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>62</EC_abs>
- <defect_size>1.75837294771776</defect_size>
- <vol_abs_CGW>[185.891533796121 683.956889277451 473.772958874703 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.63698350184104</vol_abs_WMH>
- <vol_rel_WMH>0.000474079610818193</vol_rel_WMH>
- <surf_TSA>1820.85252980985</surf_TSA>
- <vol_TIV>1343.62138194827</vol_TIV>
- <vol_rel_CGW>[0.138351127999002 0.509039896556053 0.352608975444945 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.50700689567305 0.669891974345383]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.53228259086609 0.822911791269237 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.80540494092932 0.295229362512027 0.265502779009104;2.52919744280867 0.19666028479859 0.446435025744195;3.24163283772147 0.293865294806747 0.288062195246701]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.735307837870938 0.268374510189035 0.632877557314691;4.19217139290548 0.317631818226692 0.367122442685309]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.07535405563123</vol_TIV>
- <vol_rel_CGW>[0.5 6.99209584331993 4.18263246129571 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04740796108182</vol_rel_WMH>
- <surf_TSA>8.59401765063825</surf_TSA>
- <SQR>5.72952992636535</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.191288232803345 1 1 10732.3734268785 0.562473574029671]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0455034822225571 0.0449123531579971 0.123878724873066]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[841.6315298741 430.269438761368 320.543014238266 2955.94889047823 2891.92684028349 6498.0336822048]</SPMvols0>
- <SPMvols1>[726.29446647069 402.066547994508 173.517183317647 3139.48693609904 2523.16388088616 6307.36077986956]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[14.7966003417969 33.8361015319824 51.228199005127]</T3th>
- <Tth>
- <T3th>[0 0 2.26064777374268 14.7966003417969 33.8361015319824 51.228199005127 69.4440002441406 234.520126342773]</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>[0.0181998666375875 0.0690250173211098 0.075845293700695 0 0]</dtc>
- <ll>[0.0816448283414929 0 0.0816448283414929 0;0.195249193427371 0.00958365294970527 0.204832846377076 2043.69482421875;0.195249193427371 0.00958365294970527 0.204832846377076 2043.69482421875]</ll>
- <rmsdtc>[0.0394064262509346 0.0910830125212669 0.102146193385124]</rmsdtc>
- <rmsgdt>[0.0280667785555124 0.0432515814900398 0.054066427052021]</rmsgdt>
- <rmsdt>0.102146193385124</rmsdt>
- <dt>0.075845293700695</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>[0.00857355818152428 0.0322151221334934 0.0464542470872402 0.0543899722397327 0.0610185004770756 0.0687972977757454]</dtc>
- <ll>[0.0836945723353563 0 0.0836945723353563 0;0.224104502442002 0.0126692441239316 0.236773746565934 6485.0693359375;0.203647887106231 0.0161431841616855 0.219791071267917 11618.443359375;0.184399900952635 0.0184946920570598 0.202894593009695 19942.30859375;0.168577164671739 0.0218693889969606 0.190446553668699 38257.28125;0.168577164671739 0.0218693889969606 0.190446553668699 38257.28125]</ll>
- <rmsdtc>[0.0101499632000923 0.0377756357192993 0.0586788728833199 0.0845384001731873 0.109515160322189 0.117523491382599]</rmsdtc>
- <rmsgdt>[0.00306690647266805 0.0123866312205791 0.0288835056126118 0.0507103614509106 0.0711984112858772 0.0779499337077141]</rmsgdt>
- <rmsdt>0.117523491382599</rmsdt>
- <dt>0.0687972977757454</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_42422/ds/sub-0101/sub-0101_ses-01_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 77s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 11s</item>
- <item>Estimate background 12s</item>
- <item>Initial correction 25s</item>
- <item>Refine background 5s</item>
- <item>Final correction 12s</item>
- <item>Final scaling 8s</item>
- <item>85s</item>
- <item>Correct center-of-mass 7s</item>
- <item>Affine registration 26s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 116s</item>
- <item>SPM preprocessing 1 (estimate 2): 81s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 28s</item>
- <item>Update Segmentation 27s</item>
- <item>Update Skull-Stripping 65s</item>
- <item>Update probability maps 14s</item>
- <item>134s</item>
- <item>Global intensity correction: 26s</item>
- <item>SANLM denoising after intensity normalization (medium): 12s</item>
- <item>Fast Optimized Shooting registration 45s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 5s</item>
- <item>Prepare segments (LASmod = 1.00) 20s</item>
- <item>Estimate local tissue thresholds (WM) 31s</item>
- <item>Estimate local tissue thresholds (GM) 43s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 51s</item>
- <item>162s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 10s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 22s</item>
- <item>Blood vessel detection 14s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 36s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 5s</item>
- <item>Final corrections 7s</item>
- <item>101s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 6s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>16s</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 | 0.0837 0.0000 0.0837 | 32.0000</item>
- <item>2 | 2.50 | 0.0812 0.0011 0.0823 | 29.4886</item>
- <item>3 | 2.50 | 0.0804 0.0017 0.0822 | 26.9772</item>
- <item>4 | 2.50 | 0.0801 0.0019 0.0820 | 24.6107</item>
- <item>5 | 2.50 | 0.0798 0.0020 0.0819 | 22.6548</item>
- <item>6 | 2.50 | 0.0796 0.0021 0.0817 | 20.6989</item>
- <item>7 | 2.50 | 0.0793 0.0022 0.0815 | 18.9688</item>
- <item>8 | 2.50 | 0.0791 0.0023 0.0813 | 17.4455</item>
- <item>9 | 2.50 | 0.0788 0.0024 0.0811 | 15.9223</item>
- <item>10 | 2.50 | 0.0785 0.0024 0.0809 | 14.6627</item>
- <item>11 | 2.50 | 0.0782 0.0025 0.0807 | 13.4764</item>
- <item>12 | 2.50 | 0.0779 0.0026 0.0805 | 12.3015</item>
- <item>13 | 2.50 | 0.0776 0.0027 0.0803 | 11.3776</item>
- <item>14 | 2.50 | 0.0774 0.0027 0.0801 | 10.4537</item>
- <item>15 | 2.25 | 0.0778 0.0028 0.0806 | 9.5920</item>
- <item>16 | 2.25 | 0.0747 0.0042 0.0789 | 8.8725</item>
- <item>29 | 2.00 | 0.0762 0.0019 0.0781 | 3.3283</item>
- <item>30 | 2.00 | 0.0699 0.0044 0.0744 | 3.1221</item>
- <item>31 | 2.00 | 0.0679 0.0054 0.0733 | 2.9160</item>
- <item>43 | 1.75 | 0.0671 0.0031 0.0702 | 1.5785</item>
- <item>44 | 1.75 | 0.0629 0.0054 0.0683 | 1.5194</item>
- <item>45 | 1.75 | 0.0615 0.0062 0.0676 | 1.4626</item>
- <item>57 | 1.50 | 0.0605 0.0045 0.0650 | 1.0900</item>
- <item>58 | 1.50 | 0.0573 0.0066 0.0639 | 1.0730</item>
- <item>59 | 1.50 | 0.0562 0.0073 0.0635 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 188s</item>
- <item>Prepare output 16s</item>
- <item>203s</item>
- <item>Jacobian determinant (RMS): 0.010 0.038 0.059 0.085 0.110 | 0.117523</item>
- <item>Template Matching: 0.084 0.224 0.204 0.184 0.169 | 0.168577</item>
- <item>Write result maps: 37s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 41s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 55s</item>
- <item>120s</item>
- <item>Create initial surface 94s</item>
- <item>Topology correction: 108s</item>
- <item>Surface refinement: 73s</item>
- <item>Reduction of surface collisions with optimization: 66s</item>
- <item>Spherical mapping with areal smoothing 85s</item>
- <item>Spherical registration 333s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 52s</item>
- <item>113s</item>
- <item>Create initial surface 92s</item>
- <item>Topology correction: 100s</item>
- <item>Surface refinement: 81s</item>
- <item>Reduction of surface collisions with optimization: 67s</item>
- <item>Spherical mapping with areal smoothing 86s</item>
- <item>Spherical registration 324s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5069 0.6697 mm</item>
- <item>Surface intensity / position RMSE: 0.0807 / 0.0881</item>
- <item>Euler number / defect number / defect size: 62.0 / 41.0 / 1.76%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_42422/ds/sub-0101/surf/lh.thickness.sub-0101_ses-01_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_42422/ds/sub-0101/surf/rh.thickness.sub-0101_ses-01_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_42422/ds/sub-0101/sub-0101_ses-01_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1853s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 46s</item>
- <item>ROI estimation of 'lpba40' atlas 13s</item>
- <item>ROI estimation of 'hammers' atlas 32s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 11s</item>
- <item>ROI estimation of 'aal3' atlas 18s</item>
- <item>ROI estimation of 'mori' atlas 27s</item>
- <item>ROI estimation of 'anatomy3' atlas 39s</item>
- <item>ROI estimation of 'julichbrain' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 83s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 126s</item>
- <item>Write results 127s</item>
- <item>519s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_42422/ds/sub-0101/report/catreport_sub-0101_ses-01_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 61 minute(s) and 7 second(s).</item>
- <item>Image Quality Rating (IQR): 80.38% (B-)</item>
- <item>GM volume (GMV): 50.90% (683.96 / 1343.62 ml)</item>
- <item>GM thickness (GMT): 2.51 0.67 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_42422/ds/sub-0101/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_42422/ds/sub-0101/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_42422/ds/sub-0101/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|