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- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <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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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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- <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_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>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </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>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <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>
- <gifti_dat>1</gifti_dat>
- <atlas>
- <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>
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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>
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- <item>gm</item>
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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>
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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/thalamus.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/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>
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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/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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- <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>
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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/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</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/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <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>
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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/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/var/lib/condor/execute/dir_1702337/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
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- <td>[false]</td>
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- </atlas>
- <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>
- </tr>
- <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>
- </tr>
- <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>
- </tr>
- <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>
- </tr>
- <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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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
- <new_release>0</new_release>
- <lazy>0</lazy>
- <affmod>0</affmod>
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- <shooting>
- <shootingtpm>
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- </shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.560788520124016</SurfaceDefectArea>
- <SurfaceDefectNumber>21.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0680877715349197</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0681164413690567</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>175.615768432617</res_BB>
- <tissue_mn>[13.6529998779297 99.7590026855469 276.25 428.502990722656]</tissue_mn>
- <tissue_mnr>[0.0318620875477791 0.232808187603951 0.644686281681061 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[26.6166426195632 50.9346128768867 45.3934784381561 28.2636007146309]</tissue_std>
- <tissue_stdr>[0.0641596838831902 0.12277839332819 0.10942143201828 0.068129688501358]</tissue_stdr>
- <contrast>154.231872558594</contrast>
- <contrastr>0.359931856393814</contrastr>
- <res_ECR>0.377743363380432</res_ECR>
- <NCR>0.149920597672462</NCR>
- <ICR>0.313105255365372</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.82522106170654</res_ECR>
- <res_BB>10.5</res_BB>
- <tissue_mn>[8.62400054931641 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>2.68435549736023</contrastr>
- <NCR>2.48321270942688</NCR>
- <ICR>1.23637223243713</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.140197130031</SurfaceDefectArea>
- <SurfaceDefectNumber>2.075</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.36175537109375</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.36232876777649</SurfacePositionRMSE>
- <SIQR>2.57288473260087</SIQR>
- <IQR>2.32399479413495</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>20231031-014749</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.560788520124016</SurfaceDefectArea>
- <SurfaceDefectNumber>21.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0680877715349197</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0681164413690567</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.560788520124016</defect_size>
- <vol_abs_CGW>[186.119294117647 664.336815686274 458.947854901961 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.365752941176471</vol_abs_WMH>
- <vol_rel_WMH>0.000279327809472935</vol_rel_WMH>
- <surf_TSA>1730.29887727752</surf_TSA>
- <vol_TIV>1309.40396470588</vol_TIV>
- <vol_rel_CGW>[0.142140469354278 0.507358182496032 0.35050134814969 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.68693840749424 0.635853765975103]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.68305230140686 0.788957880178162 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.09615715479211 0.259590189715879 0.310168754471362;2.72433858776502 0.183830489741634 0.419094645587555;3.40452712726515 0.281971751143352 0.270736599941083]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.959835936454109 0.367182866317884 0.592227695675972;4.34234912725103 0.331473705349436 0.407772304324028]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.1930605836397</vol_TIV>
- <vol_rel_CGW>[0.5 6.96189264540287 4.14477995958495 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02793278094729</vol_rel_WMH>
- <surf_TSA>8.53636948055572</surf_TSA>
- <SQR>5.7043504177634</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.648 0.375199856831715]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00166708661708981 0.00104845792520791 0.288178235292435]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[776.192364705882 414.513470588235 267.399960784314 417.942878431373 843.989168627451 7020.63676078431]</SPMvols0>
- <SPMvols1>[702.890019607843 393.72171372549 165.720054901961 355.679470588235 669.481662745098 7084.23390588235]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[114.813598632812 289.72900390625 421.219512939453]</T3th>
- <Tth>
- <T3th>[-6.08534002304077 -6.08534097671509 7.16960763931274 114.813598632812 289.72900390625 421.219512939453 574.422485351562 1123.56604003906]</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>[0.0189510900527239 0.0636971145868301 0.0694493874907494 0 0]</dtc>
- <ll>[0.0788980448136286 0 0.0788980448136286 0;0.189211384016497 0.00832139572748044 0.197532779743978 1774.52099609375;0.189211384016497 0.00832139572748044 0.197532779743978 1774.52099609375]</ll>
- <rmsdtc>[0.0428981557488441 0.0838682055473328 0.0934021770954132]</rmsdtc>
- <rmsgdt>[0.0306774619966745 0.038837306201458 0.0481487326323986]</rmsgdt>
- <rmsdt>0.0934021770954132</rmsdt>
- <dt>0.0694493874907494</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>[0.00872012600302696 0.0310973022133112 0.0427903831005096 0.0498779900372028 0.0547688081860542 0.0608636327087879]</dtc>
- <ll>[0.0801796356993699 0 0.0801796356993699 0;0.209741834554335 0.011373044490232 0.221114879044567 5821.5771484375;0.190258481864968 0.0142593984208267 0.204517880285795 10262.66015625;0.171427814595946 0.016342963701413 0.187770778297359 17622.16015625;0.158346364341559 0.0173448635366904 0.17569122787825 30342.2890625;0.158346364341559 0.0173448635366904 0.17569122787825 30342.2890625]</ll>
- <rmsdtc>[0.0101451482623816 0.0362697280943394 0.0536323413252831 0.0749509334564209 0.0966443791985512 0.101459369063377]</rmsdtc>
- <rmsgdt>[0.00305541814304888 0.0117248315364122 0.0258810445666313 0.0450885482132435 0.0633684322237968 0.0676794499158859]</rmsgdt>
- <rmsdt>0.101459369063377</rmsdt>
- <dt>0.0608636327087879</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025272/ses-2/sub-0025272_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 62s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>39s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 11s</item>
- <item>Use initial fine affine registration. 68s</item>
- <item>SPM preprocessing 1 (estimate 2): 61s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 18s</item>
- <item>Update Segmentation 19s</item>
- <item>Update Skull-Stripping 39s</item>
- <item>Update probability maps 8s</item>
- <item>84s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 32s</item>
- <item>Fast Optimized Shooting registration 36s</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) 15s</item>
- <item>Estimate local tissue thresholds (WM) 20s</item>
- <item>Estimate local tissue thresholds (GM) 31s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 44s</item>
- <item>117s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 14s</item>
- <item>Blood vessel detection 10s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 27s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 4s</item>
- <item>71s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>12s</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 | 0.0802 0.0000 0.0802 | 32.0000</item>
- <item>2 | 2.50 | 0.0780 0.0011 0.0791 | 29.4886</item>
- <item>3 | 2.50 | 0.0774 0.0016 0.0790 | 26.9772</item>
- <item>4 | 2.50 | 0.0771 0.0018 0.0789 | 24.6107</item>
- <item>5 | 2.50 | 0.0768 0.0019 0.0787 | 22.6548</item>
- <item>6 | 2.50 | 0.0766 0.0020 0.0786 | 20.6989</item>
- <item>7 | 2.50 | 0.0764 0.0020 0.0784 | 18.9688</item>
- <item>8 | 2.50 | 0.0762 0.0021 0.0783 | 17.4455</item>
- <item>9 | 2.50 | 0.0759 0.0022 0.0781 | 15.9223</item>
- <item>10 | 2.50 | 0.0757 0.0022 0.0779 | 14.6627</item>
- <item>11 | 2.50 | 0.0754 0.0023 0.0777 | 13.4764</item>
- <item>12 | 2.50 | 0.0752 0.0023 0.0775 | 12.3015</item>
- <item>13 | 2.50 | 0.0749 0.0024 0.0773 | 11.3776</item>
- <item>14 | 2.50 | 0.0747 0.0025 0.0771 | 10.4537</item>
- <item>15 | 2.25 | 0.0726 0.0025 0.0751 | 9.5920</item>
- <item>16 | 2.25 | 0.0699 0.0038 0.0737 | 8.8725</item>
- <item>29 | 2.00 | 0.0707 0.0017 0.0724 | 3.3283</item>
- <item>30 | 2.00 | 0.0652 0.0039 0.0691 | 3.1221</item>
- <item>31 | 2.00 | 0.0634 0.0048 0.0682 | 2.9160</item>
- <item>43 | 1.75 | 0.0622 0.0027 0.0650 | 1.5785</item>
- <item>44 | 1.75 | 0.0584 0.0047 0.0631 | 1.5194</item>
- <item>45 | 1.75 | 0.0571 0.0054 0.0626 | 1.4626</item>
- <item>57 | 1.50 | 0.0556 0.0039 0.0595 | 1.0900</item>
- <item>58 | 1.50 | 0.0528 0.0058 0.0586 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 164s</item>
- <item>Prepare output 12s</item>
- <item>177s</item>
- <item>Jacobian determinant (RMS): 0.010 0.036 0.054 0.075 0.097 | 0.101459</item>
- <item>Template Matching: 0.080 0.210 0.190 0.171 0.158 | 0.158346</item>
- <item>Write result maps: 65s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 32s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 51s</item>
- <item>105s</item>
- <item>Create initial surface 91s</item>
- <item>Topology correction: 85s</item>
- <item>Surface refinement: 98s</item>
- <item>Reduction of surface collisions with optimization: 66s</item>
- <item>Spherical mapping with areal smoothing 98s</item>
- <item>Spherical registration 351s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 31s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 54s</item>
- <item>108s</item>
- <item>Create initial surface 91s</item>
- <item>Topology correction: 88s</item>
- <item>Surface refinement: 87s</item>
- <item>Reduction of surface collisions with optimization: 67s</item>
- <item>Spherical mapping with areal smoothing 92s</item>
- <item>Spherical registration 334s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6869 0.6357 mm</item>
- <item>Surface intensity / position RMSE: 0.0681 / 0.0681</item>
- <item>Euler number / defect number / defect size: 18.0 / 21.5 / 0.56%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-2/surf/lh.thickness.sub-0025272_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-2/surf/rh.thickness.sub-0025272_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-2/sub-0025272_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 1864s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 29s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 20s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 12s</item>
- <item>ROI estimation of 'mori' atlas 17s</item>
- <item>ROI estimation of 'anatomy3' atlas 24s</item>
- <item>ROI estimation of 'julichbrain' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 55s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 83s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 9s</item>
- <item>362s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-2/report/catreport_sub-0025272_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 53 minute(s) and 34 second(s).</item>
- <item>Image Quality Rating (IQR): 81.76% (B-)</item>
- <item>GM volume (GMV): 50.74% (664.34 / 1309.40 ml)</item>
- <item>GM thickness (GMT): 2.69 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1702337/ds/UPSM_1/sub-0025272/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|