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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>
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- <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>
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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>
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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>
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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>
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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>
- <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>
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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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- <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>
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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_1682866/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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- <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>
- <NB>0</NB>
- <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>
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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>
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- </darteltpms>
- <shootingtpms>
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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>
- </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>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.226243983255885</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.069781705737114</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0653362646698952</SurfacePositionRMSE>
- <res_vx_vol>[1.1999999710169 0.499999986111463 0.499999996905874]</res_vx_vol>
- <res_vx_voli>[0.79999998039919 0.800000002014354 0.800000007040566]</res_vx_voli>
- <res_RMS>0.804155854184562</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[21.2469997406006 60.5050010681152 227.464996337891 373.177001953125]</tissue_mn>
- <tissue_mnr>[0.0569354481995106 0.162134855985641 0.609536468982697 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[13.1997374935459 39.7315421559983 41.0227095820838 24.8082511758609]</tissue_std>
- <tissue_stdr>[0.0375067144632339 0.112896151840687 0.116564974188805 0.0704920068383217]</tissue_stdr>
- <contrast>130.808227539062</contrast>
- <contrastr>0.350525945425034</contrastr>
- <res_ECR>0.325151085853577</res_ECR>
- <NCR>0.161121785640717</NCR>
- <ICR>0</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.39999994203381 0.999999972222926 0.999999993811747]</res_vx_vol>
- <res_RMS>1.60831170836912</res_RMS>
- <res_ECR>2.55689334869385</res_ECR>
- <res_BB>NaN</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>2.82544422149658</contrastr>
- <NCR>2.64401054382324</NCR>
- <ICR>0.5</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.05656099581397</SurfaceDefectArea>
- <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.39563417434692</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.30672526359558</SurfacePositionRMSE>
- <SIQR>2.47762769097539</SIQR>
- <IQR>2.43020299946654</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>20231031-011523</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.226243983255885</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.069781705737114</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0653362646698952</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>0.226243983255885</defect_size>
- <vol_abs_CGW>[239.938384162535 798.731795588475 593.454586184709 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.736053198140217</vol_abs_WMH>
- <vol_rel_WMH>0.000450978511877569</vol_rel_WMH>
- <surf_TSA>2329.76872692525</surf_TSA>
- <vol_TIV>1632.12476593572</vol_TIV>
- <vol_rel_CGW>[0.147009829867373 0.489381579312382 0.363608590820245 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.48369399095447 0.602415823331368]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.47469830513 0.706504696539433 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.90095993110333 0.234437006177406 0.310502258521274;2.51253330713761 0.174174138585678 0.42992661824799;3.1568433273444 0.257037995920592 0.259571123230735]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.905106702839867 0.379768992557313 0.513681698064956;4.06451380835825 0.360880767448526 0.486318301935044]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.18147717060459</vol_TIV>
- <vol_rel_CGW>[0.5 6.63903698477698 4.38018302478889 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04509785118776</vol_rel_WMH>
- <surf_TSA>8.62399153744979</surf_TSA>
- <SQR>5.45316425617915</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[2.54313151041667e-08 1 1 11796.4790144133 0.396925203986878]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00124897004570812 0.00108302524313331 0.0754342675209045]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[980.341777194426 501.414190598019 522.684802647034 1223.39470550414 1031.34442963582 8195.90374739392]</SPMvols0>
- <SPMvols1>[837.377577165306 473.535977694932 268.945856219364 812.03896655031 948.609260467637 8458.99941137667]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[75.7228012084961 237.644607543945 377.363311767578]</T3th>
- <Tth>
- <T3th>[-142.669815063477 -72.3232192993164 1.69979095458984 75.7228012084961 237.644607543945 377.363311767578 528.18359375 1037.02026367188]</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>[0.0229760035872459 0.0859090611338615 0.0960004404187202 0 0]</dtc>
- <ll>[0.0867426255170037 0 0.0867426255170037 0;0.19582294587757 0.0120237998458661 0.207846745723436 2564.05126953125;0.19582294587757 0.0120237998458661 0.207846745723436 2564.05126953125]</ll>
- <rmsdtc>[0.0513254031538963 0.113591782748699 0.125923350453377]</rmsdtc>
- <rmsgdt>[0.0365906357765198 0.0492842420935631 0.0601878426969051]</rmsgdt>
- <rmsdt>0.125923350453377</rmsdt>
- <dt>0.0960004404187202</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>[0.0103677567094564 0.038453821092844 0.0547824501991272 0.0638308748602867 0.0703674405813217 0.0792635530233383]</dtc>
- <ll>[0.0857914649540793 0 0.0857914649540793 0;0.223797985347985 0.0148135588369963 0.238611544184982 7582.6904296875;0.201712824886899 0.0177030827521981 0.219415907639097 12741.12109375;0.180388998555096 0.0199592749730587 0.200348273528154 21521.52734375;0.162439216813302 0.0231173414542405 0.185556558267542 40440.390625;0.162439216813302 0.0231173414542405 0.185556558267542 40440.390625]</ll>
- <rmsdtc>[0.0121380351483822 0.0446629673242569 0.0670833438634872 0.0942248702049255 0.1180374994874 0.124591216444969]</rmsdtc>
- <rmsgdt>[0.00342790293507278 0.0134491631761193 0.0294072013348341 0.0509662441909313 0.0700263381004333 0.0752317383885384]</rmsgdt>
- <rmsdt>0.124591216444969</rmsdt>
- <dt>0.0792635530233383</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026032/ses-2/sub-0026032_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 354s</item>
- <item>Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 3s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 15s</item>
- <item>Estimate background 13s</item>
- <item>Initial correction 15s</item>
- <item>Refine background 7s</item>
- <item>Final correction 13s</item>
- <item>Final scaling 12s</item>
- <item>90s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 20s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 178s</item>
- <item>SPM preprocessing 1 (estimate 2): 63s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 40s</item>
- <item>Update Segmentation 46s</item>
- <item>Update Skull-Stripping 107s</item>
- <item>Update probability maps 21s</item>
- <item>215s</item>
- <item>Global intensity correction: 41s</item>
- <item>SANLM denoising after intensity normalization (medium): 79s</item>
- <item>Fast Optimized Shooting registration 60s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 11s</item>
- <item>Prepare partitions 6s</item>
- <item>Prepare segments (LASmod = 1.00) 41s</item>
- <item>Estimate local tissue thresholds (WM) 52s</item>
- <item>Estimate local tissue thresholds (GM) 78s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 110s</item>
- <item>307s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 20s</item>
- <item>Major structures 9s</item>
- <item>Ventricle detection 40s</item>
- <item>Blood vessel detection 30s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.03) 69s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 5s</item>
- <item>Side alignment 10s</item>
- <item>Final corrections 11s</item>
- <item>194s</item>
- <item>Blood vessel correction (BVCstr=0.50): 4s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 76s</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) 11s</item>
- <item>Level 1 cleanup (brain masking) 7s</item>
- <item>Level 2 cleanup (CSF correction) 4s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
- <item>30s</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 | 0.0858 0.0000 0.0858 | 32.0000</item>
- <item>2 | 2.50 | 0.0827 0.0013 0.0840 | 29.4886</item>
- <item>3 | 2.50 | 0.0818 0.0020 0.0838 | 26.9772</item>
- <item>4 | 2.50 | 0.0813 0.0023 0.0836 | 24.6107</item>
- <item>5 | 2.50 | 0.0809 0.0024 0.0834 | 22.6548</item>
- <item>6 | 2.50 | 0.0806 0.0025 0.0832 | 20.6989</item>
- <item>7 | 2.50 | 0.0803 0.0026 0.0830 | 18.9688</item>
- <item>8 | 2.50 | 0.0800 0.0028 0.0827 | 17.4455</item>
- <item>9 | 2.50 | 0.0796 0.0028 0.0825 | 15.9223</item>
- <item>10 | 2.50 | 0.0793 0.0030 0.0822 | 14.6627</item>
- <item>11 | 2.50 | 0.0789 0.0030 0.0820 | 13.4764</item>
- <item>12 | 2.50 | 0.0785 0.0031 0.0817 | 12.3015</item>
- <item>13 | 2.50 | 0.0782 0.0032 0.0814 | 11.3776</item>
- <item>14 | 2.50 | 0.0778 0.0033 0.0811 | 10.4537</item>
- <item>15 | 2.25 | 0.0778 0.0034 0.0812 | 9.5920</item>
- <item>16 | 2.25 | 0.0746 0.0049 0.0795 | 8.8725</item>
- <item>29 | 2.00 | 0.0759 0.0022 0.0781 | 3.3283</item>
- <item>30 | 2.00 | 0.0695 0.0048 0.0743 | 3.1221</item>
- <item>31 | 2.00 | 0.0672 0.0059 0.0731 | 2.9160</item>
- <item>43 | 1.75 | 0.0663 0.0034 0.0697 | 1.5785</item>
- <item>44 | 1.75 | 0.0617 0.0058 0.0675 | 1.5194</item>
- <item>45 | 1.75 | 0.0601 0.0067 0.0668 | 1.4626</item>
- <item>57 | 1.50 | 0.0586 0.0049 0.0634 | 1.0900</item>
- <item>58 | 1.50 | 0.0553 0.0070 0.0623 | 1.0730</item>
- <item>59 | 1.50 | 0.0541 0.0077 0.0619 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 207s</item>
- <item>Prepare output 22s</item>
- <item>229s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.067 0.094 0.118 | 0.124591</item>
- <item>Template Matching: 0.086 0.224 0.202 0.180 0.162 | 0.162439</item>
- <item>Write result maps: 292s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 45s</item>
- <item>CSF distance: 23s</item>
- <item>PBT2x thickness: 67s</item>
- <item>144s</item>
- <item>Create initial surface 122s</item>
- <item>Topology correction: 131s</item>
- <item>Surface refinement: 111s</item>
- <item>Reduction of surface collisions with optimization: 109s</item>
- <item>Spherical mapping with areal smoothing 137s</item>
- <item>Spherical registration 345s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 56s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 67s</item>
- <item>154s</item>
- <item>Create initial surface 118s</item>
- <item>Topology correction: 138s</item>
- <item>Surface refinement: 133s</item>
- <item>Reduction of surface collisions with optimization: 101s</item>
- <item>Spherical mapping with areal smoothing 131s</item>
- <item>Spherical registration 351s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4836 0.6024 mm</item>
- <item>Surface intensity / position RMSE: 0.0698 / 0.0653</item>
- <item>Euler number / defect number / defect size: 14.0 / 10.5 / 0.23%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/surf/lh.thickness.sub-0026032_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/surf/rh.thickness.sub-0026032_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/sub-0026032_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2439s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 19s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 71s</item>
- <item>ROI estimation of 'lpba40' atlas 20s</item>
- <item>ROI estimation of 'hammers' atlas 51s</item>
- <item>ROI estimation of 'thalamus' atlas 4s</item>
- <item>ROI estimation of 'ibsr' atlas 18s</item>
- <item>ROI estimation of 'aal3' atlas 29s</item>
- <item>ROI estimation of 'mori' atlas 43s</item>
- <item>ROI estimation of 'anatomy3' atlas 62s</item>
- <item>ROI estimation of 'julichbrain' atlas 81s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 33s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 56s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 125s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 189s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 16s</item>
- <item>Write results 17s</item>
- <item>820s</item>
- <item>Quality check: 66s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/report/catreport_sub-0026032_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 95 minute(s) and 4 second(s).</item>
- <item>Image Quality Rating (IQR): 80.70% (B-)</item>
- <item>GM volume (GMV): 48.94% (798.73 / 1632.12 ml)</item>
- <item>GM thickness (GMT): 2.48 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|