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- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
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- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
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- <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>
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- <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>
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- <reduce_mesh>1</reduce_mesh>
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- <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>
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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>
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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>
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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>
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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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- <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>
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- <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>
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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>
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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_2217288/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- <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>
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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>
- </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>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- <pbtmethod>pbt2x</pbtmethod>
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- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
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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>
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- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0969254763792513</SurfaceDefectArea>
- <SurfaceDefectNumber>5.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0563118159770966</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0524330213665962</SurfacePositionRMSE>
- <res_vx_vol>[0.999999978530028 0.999999979275968 1.00000000836916]</res_vx_vol>
- <res_vx_voli>[1.00000003809182 0.999999979459748 1.00000000886588]</res_vx_voli>
- <res_RMS>0.999999988725052</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[10.8414993286133 69.6029968261719 206.430999755859 324.071990966797]</tissue_mn>
- <tissue_mnr>[0.0334539860486984 0.214776337146759 0.636991202831268 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[12.9066263318184 29.7543506478682 36.3894332945822 23.6400276055685]</tissue_std>
- <tissue_stdr>[0.0412048846483231 0.0949918702244759 0.11617461591959 0.0754716694355011]</tissue_stdr>
- <contrast>116.088645935059</contrast>
- <contrastr>0.35821869969368</contrastr>
- <res_ECR>0.396119654178619</res_ECR>
- <NCR>0.128294765949249</NCR>
- <ICR>0.23990561068058</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999995706006 1.99999995855194 2.00000001673832]</res_vx_vol>
- <res_RMS>1.9999999774501</res_RMS>
- <res_ECR>2.91897773742676</res_ECR>
- <res_BB>1</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>2.71005272865295</contrastr>
- <NCR>2.17276430130005</NCR>
- <ICR>1.05482542514801</ICR>
- <SurfaceEulerNumber>1.40816326530612</SurfaceEulerNumber>
- <SurfaceDefectArea>1.02423136909481</SurfaceDefectArea>
- <SurfaceDefectNumber>1.275</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.12623631954193</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.0486603975296</SurfacePositionRMSE>
- <SIQR>2.58724594900061</SIQR>
- <IQR>2.09869606108305</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>20231031-020747</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0969254763792513</SurfaceDefectArea>
- <SurfaceDefectNumber>5.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0563118159770966</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0524330213665962</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>10</EC_abs>
- <defect_size>0.0969254763792513</defect_size>
- <vol_abs_CGW>[364.722390027187 513.551546900049 373.304280449977 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.1757333643932</vol_abs_WMH>
- <vol_rel_WMH>0.000939400628797329</vol_rel_WMH>
- <surf_TSA>1589.40504818365</surf_TSA>
- <vol_TIV>1251.57821737721</vol_TIV>
- <vol_rel_CGW>[0.291409985379494 0.410323174189016 0.298266840431489 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.29729795894421 0.605351985198061]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.28276371955872 0.742985174272913 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.74190714941609 0.263545093126423 0.325626249744147;2.3474003949702 0.175056081192794 0.465070143120306;3.03659584822183 0.278445876360436 0.209303607135547]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.799538772835513 0.2041561349346 0.574570755246325;4.03866951366868 0.38416371169753 0.425429244753675]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.50718380717997</vol_TIV>
- <vol_rel_CGW>[3.08351266845356 5.21916620310733 3.20666020889888 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.09394006287973</vol_rel_WMH>
- <surf_TSA>8.25433586886987</surf_TSA>
- <SQR>4.28652414704868</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10813.4396342371 0.483908836026982]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00122040149290115 0.00107250665314496 0.0363682173192501]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[628.351475422965 334.621969624168 521.877166727833 869.054156291516 667.554547046845 8287.45141893322]</SPMvols0>
- <SPMvols1>[552.433473417406 311.544263132162 336.386785357065 663.604664589558 593.876960786746 8356.19546388652]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[76.8199005126953 214.461700439453 314.102600097656]</T3th>
- <Tth>
- <T3th>[-3.97652006149292 -3.97651982307434 3.73195147514343 76.8199005126953 214.461700439453 314.102600097656 432.743957519531 742.910827636719]</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>[0.0243770629167557 0.112952291965485 0.132622584700584 0 0]</dtc>
- <ll>[0.101373160348124 0 0.101373160348124 0;0.213613778030744 0.0216523682226797 0.235266146253423 4617.32421875;0.213613778030744 0.0216523682226797 0.235266146253423 4617.32421875]</ll>
- <rmsdtc>[0.0528571717441082 0.161455601453781 0.193175882101059]</rmsdtc>
- <rmsgdt>[0.0378758832812309 0.0871598497033119 0.117091305553913]</rmsgdt>
- <rmsdt>0.193175882101059</rmsdt>
- <dt>0.132622584700584</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>[0.0120701007544994 0.0475780442357063 0.0816383734345436 0.0943317636847496 0.10420785844326 0.12376444786787]</dtc>
- <ll>[0.102627518690675 0 0.102627518690675 0;0.0958121693121693 0.00512470110907611 0.100936870421245 7869.619140625;0.222224784010827 0.0348307753005716 0.257055559311398 25068.126953125;0.197634560203733 0.0328287050368553 0.230463265240589 35398.2734375;0.176761994291604 0.0352888726932186 0.212050866984822 61732.6953125;0.176761994291604 0.0352888726932186 0.212050866984822 61732.6953125]</ll>
- <rmsdtc>[0.0142399566248059 0.0590554475784302 0.118327714502811 0.158664837479591 0.198879912495613 0.210228323936462]</rmsdtc>
- <rmsgdt>[0.00445826258510351 0.0214684139937162 0.055925365537405 0.0864108800888062 0.114396400749683 0.127002447843552]</rmsgdt>
- <rmsdt>0.210228323936462</rmsdt>
- <dt>0.12376444786787</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026184/ses-1/sub-0026184_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 57s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>41s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 97s</item>
- <item>SPM preprocessing 1 (estimate 2): 91s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 21s</item>
- <item>Update Skull-Stripping 47s</item>
- <item>Update probability maps 10s</item>
- <item>96s</item>
- <item>Global intensity correction: 18s</item>
- <item>SANLM denoising after intensity normalization (medium): 29s</item>
- <item>Fast Optimized Shooting registration 42s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.09) 16s</item>
- <item>Estimate local tissue thresholds (WM) 19s</item>
- <item>Estimate local tissue thresholds (GM) 31s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 49s</item>
- <item>125s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 14s</item>
- <item>Blood vessel detection 10s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.41) 21s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>67s</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 0.05,0.68 0.08,0.98 0.04]</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 | 0.1026 0.0000 0.1026 | 32.0000</item>
- <item>2 | 2.50 | 0.0984 0.0017 0.1001 | 29.4886</item>
- <item>3 | 2.50 | 0.0971 0.0026 0.0997 | 26.9772</item>
- <item>4 | 2.50 | 0.0964 0.0030 0.0994 | 24.6107</item>
- <item>5 | 2.50 | 0.0959 0.0033 0.0991 | 22.6548</item>
- <item>6 | 2.50 | 0.0954 0.0035 0.0988 | 20.6989</item>
- <item>7 | 2.50 | 0.0949 0.0037 0.0985 | 18.9688</item>
- <item>8 | 2.50 | 0.0943 0.0039 0.0982 | 17.4455</item>
- <item>9 | 2.50 | 0.0938 0.0040 0.0978 | 15.9223</item>
- <item>10 | 2.50 | 0.0932 0.0042 0.0974 | 14.6627</item>
- <item>11 | 2.50 | 0.0926 0.0044 0.0970 | 13.4764</item>
- <item>12 | 2.50 | 0.0920 0.0046 0.0966 | 12.3015</item>
- <item>13 | 2.50 | 0.0914 0.0048 0.0962 | 11.3776</item>
- <item>14 | 2.50 | 0.0908 0.0049 0.0958 | 10.4537</item>
- <item>15 | 2.25 | 0.0958 0.0051 0.1009 | 9.5920</item>
- <item>16 | 2.25 | 0.0905 0.0079 0.0984 | 8.8725</item>
- <item>17 | 2.25 | 0.0883 0.0089 0.0972 | 8.1530</item>
- <item>18 | 2.25 | 0.0867 0.0095 0.0962 | 7.5234</item>
- <item>19 | 2.25 | 0.0855 0.0098 0.0953 | 6.9630</item>
- <item>20 | 2.25 | 0.0844 0.0099 0.0943 | 6.4027</item>
- <item>21 | 2.25 | 0.0833 0.0101 0.0935 | 5.9447</item>
- <item>22 | 2.25 | 0.0824 0.0102 0.0926 | 5.5083</item>
- <item>23 | 2.25 | 0.0815 0.0102 0.0917 | 5.0803</item>
- <item>24 | 2.25 | 0.0806 0.0103 0.0909 | 4.7404</item>
- <item>25 | 2.25 | 0.0798 0.0103 0.0900 | 4.4005</item>
- <item>26 | 2.25 | 0.0790 0.0103 0.0892 | 4.0868</item>
- <item>27 | 2.25 | 0.0782 0.0103 0.0885 | 3.8221</item>
- <item>28 | 2.25 | 0.0775 0.0102 0.0877 | 3.5574</item>
- <item>29 | 2.00 | 0.0795 0.0099 0.0894 | 3.3283</item>
- <item>30 | 2.00 | 0.0764 0.0111 0.0875 | 3.1221</item>
- <item>31 | 2.00 | 0.0751 0.0114 0.0865 | 2.9160</item>
- <item>32 | 2.00 | 0.0741 0.0116 0.0857 | 2.7495</item>
- <item>43 | 1.75 | 0.0733 0.0067 0.0801 | 1.5785</item>
- <item>44 | 1.75 | 0.0677 0.0100 0.0777 | 1.5194</item>
- <item>45 | 1.75 | 0.0659 0.0109 0.0768 | 1.4626</item>
- <item>57 | 1.50 | 0.0644 0.0081 0.0725 | 1.0900</item>
- <item>58 | 1.50 | 0.0602 0.0110 0.0712 | 1.0730</item>
- <item>59 | 1.50 | 0.0589 0.0118 0.0707 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 254s</item>
- <item>Prepare output 13s</item>
- <item>268s</item>
- <item>Jacobian determinant (RMS): 0.014 0.059 0.118 0.159 0.199 | 0.210228</item>
- <item>Template Matching: 0.103 0.096 0.222 0.198 0.177 | 0.176762</item>
- <item>Write result maps: 46s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 48s</item>
- <item>101s</item>
- <item>Create initial surface 86s</item>
- <item>Topology correction: 78s</item>
- <item>Surface refinement: 68s</item>
- <item>Reduction of surface collisions with optimization: 52s</item>
- <item>Spherical mapping with areal smoothing 81s</item>
- <item>Spherical registration 331s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 34s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 47s</item>
- <item>104s</item>
- <item>Create initial surface 88s</item>
- <item>Topology correction: 83s</item>
- <item>Surface refinement: 64s</item>
- <item>Reduction of surface collisions with optimization: 53s</item>
- <item>Spherical mapping with areal smoothing 97s</item>
- <item>Spherical registration 358s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.2972 0.6050 mm</item>
- <item>Surface intensity / position RMSE: 0.0563 / 0.0524</item>
- <item>Euler number / defect number / defect size: 10.0 / 5.5 / 0.10%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-1/surf/lh.thickness.sub-0026184_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-1/surf/rh.thickness.sub-0026184_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-1/sub-0026184_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 1746s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 34s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 23s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 8s</item>
- <item>ROI estimation of 'aal3' atlas 14s</item>
- <item>ROI estimation of 'mori' atlas 20s</item>
- <item>ROI estimation of 'anatomy3' atlas 28s</item>
- <item>ROI estimation of 'julichbrain' atlas 38s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 60s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 90s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>387s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-1/report/catreport_sub-0026184_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 54 minute(s) and 40 second(s).</item>
- <item>Image Quality Rating (IQR): 84.01% (B)</item>
- <item>GM volume (GMV): 41.03% (513.55 / 1251.58 ml)</item>
- <item>GM thickness (GMT): 2.30 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2217288/ds/UM/sub-0026184/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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