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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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- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
- <tol>0.0001</tol>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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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_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>
- <item>gm</item>
- <item>wm</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>
- </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>
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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>
- </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>
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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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- <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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- <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_612028/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>
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- <shooting>
- <shootingtpm>
- <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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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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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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- </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>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.398423329778823</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0676626563072205</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0648740082979202</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>169.92463684082</res_BB>
- <tissue_mn>[161.328491210938 473.679992675781 1524.67895507812 2417.19506835938]</tissue_mn>
- <tissue_mnr>[0.0667420253157616 0.19596266746521 0.630763709545135 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[75.6318539382112 255.079642294335 256.0541368505 165.075858490464]</tissue_std>
- <tissue_stdr>[0.0335267372429371 0.113073900341988 0.113505877554417 0.0731762498617172]</tissue_stdr>
- <contrast>856.182312011719</contrast>
- <contrastr>0.354204893112183</contrastr>
- <res_ECR>0.368488788604736</res_ECR>
- <NCR>0.135566100478172</NCR>
- <ICR>0.231319919228554</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.77800416946411</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>2.77025985717773</contrastr>
- <NCR>2.2771475315094</NCR>
- <ICR>1.03353154659271</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.09960583244471</SurfaceDefectArea>
- <SurfaceDefectNumber>1.575</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.35325312614441</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.29748010635376</SurfacePositionRMSE>
- <SIQR>2.49645748819056</SIQR>
- <IQR>2.16879378932178</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>20231031-005712</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.398423329778823</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0676626563072205</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0648740082979202</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.398423329778823</defect_size>
- <vol_abs_CGW>[219.647956862745 627.092976470588 418.151082352941 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.251450980392157</vol_abs_WMH>
- <vol_rel_WMH>0.00019879244810928</vol_rel_WMH>
- <surf_TSA>1777.69216746479</surf_TSA>
- <vol_TIV>1264.89201568627</vol_TIV>
- <vol_rel_CGW>[0.173649571772792 0.495767993389029 0.330582434838179 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.46413252316156 0.610803545145835]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.44355487823486 0.714315173975083 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.88396512647734 0.245843033582866 0.307572323876672;2.47514839349347 0.172196885591097 0.431124447428795;3.13329395130842 0.262883007598028 0.261303228694533]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.911750111695084 0.294367474259289 0.512097922003985;4.04817979120643 0.335695413276324 0.487902077996015]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.42273364534262</vol_TIV>
- <vol_rel_CGW>[0.968562711436635 6.75373551345239 3.78704085557075 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01987924481093</vol_rel_WMH>
- <surf_TSA>8.57328690671878</surf_TSA>
- <SQR>5.52969020605131</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10223.616 0.523346877546387]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00148230267222971 0.00130386929959059 0.0647809132933617]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[759.665309803922 371.358117647059 348.310811764706 533.606737254902 1228.4910627451 7529.26447843137]</SPMvols0>
- <SPMvols1>[673.3518 348.520768627451 210.772768627451 432.258462745098 854.773152941176 7703.96038039216]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[561.543090820312 1609.06005859375 2399.21142578125]</T3th>
- <Tth>
- <T3th>[-34.115161895752 -34.115161895752 45.5109901428223 561.543090820312 1609.06005859375 2399.21142578125 3318.04565429688 7667.68408203125]</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>[0.0227505322545767 0.0774949193000793 0.0859683752059937 0 0]</dtc>
- <ll>[0.0866400820582139 0 0.0866400820582139 0;0.200188718065351 0.0104452730799351 0.210633991145286 2227.43359375;0.200188718065351 0.0104452730799351 0.210633991145286 2227.43359375]</ll>
- <rmsdtc>[0.0499183312058449 0.103047311306 0.11415708065033]</rmsdtc>
- <rmsgdt>[0.0357024036347866 0.0467157326638699 0.0576671846210957]</rmsgdt>
- <rmsdt>0.11415708065033</rmsdt>
- <dt>0.0859683752059937</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>[0.0113461688160896 0.0407823175191879 0.0560419633984566 0.0641317367553711 0.0698921009898186 0.07854313403368]</dtc>
- <ll>[0.0873487523476538 0 0.0873487523476538 0;0.222517658730159 0.0158183216956654 0.238335980425824 8097.00341796875;0.200649400385154 0.0172048175824149 0.217854217967569 12382.513671875;0.180599665483292 0.0184797955374432 0.199079461020735 19926.24609375;0.16676161843836 0.0193157841784934 0.186077402616853 33790.125;0.16676161843836 0.0193157841784934 0.186077402616853 33790.125]</ll>
- <rmsdtc>[0.0132524548098445 0.0469771549105644 0.0683466866612434 0.0917742252349854 0.114779278635979 0.119704194366932]</rmsdtc>
- <rmsgdt>[0.00344592542387545 0.0132121965289116 0.0289777256548405 0.0479715242981911 0.0657313168048859 0.0701226815581322]</rmsgdt>
- <rmsdt>0.119704194366932</rmsdt>
- <dt>0.07854313403368</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027271/ses-2/sub-0027271_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 50s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>31s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 67s</item>
- <item>SPM preprocessing 1 (estimate 2): 41s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 14s</item>
- <item>Update Segmentation 16s</item>
- <item>Update Skull-Stripping 34s</item>
- <item>Update probability maps 7s</item>
- <item>72s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 22s</item>
- <item>Fast Optimized Shooting registration 29s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 12s</item>
- <item>Estimate local tissue thresholds (WM) 15s</item>
- <item>Estimate local tissue thresholds (GM) 23s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 35s</item>
- <item>92s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 11s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 19s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>55s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s</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) 4s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>9s</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 | 0.0873 0.0000 0.0873 | 32.0000</item>
- <item>2 | 2.50 | 0.0838 0.0014 0.0853 | 29.4886</item>
- <item>3 | 2.50 | 0.0828 0.0022 0.0850 | 26.9772</item>
- <item>4 | 2.50 | 0.0823 0.0025 0.0848 | 24.6107</item>
- <item>5 | 2.50 | 0.0819 0.0027 0.0846 | 22.6548</item>
- <item>6 | 2.50 | 0.0815 0.0028 0.0843 | 20.6989</item>
- <item>7 | 2.50 | 0.0812 0.0029 0.0841 | 18.9688</item>
- <item>8 | 2.50 | 0.0808 0.0030 0.0838 | 17.4455</item>
- <item>9 | 2.50 | 0.0804 0.0031 0.0835 | 15.9223</item>
- <item>10 | 2.50 | 0.0800 0.0032 0.0833 | 14.6627</item>
- <item>11 | 2.50 | 0.0796 0.0033 0.0830 | 13.4764</item>
- <item>12 | 2.50 | 0.0793 0.0034 0.0827 | 12.3015</item>
- <item>13 | 2.50 | 0.0788 0.0035 0.0824 | 11.3776</item>
- <item>14 | 2.50 | 0.0784 0.0036 0.0820 | 10.4537</item>
- <item>15 | 2.25 | 0.0774 0.0037 0.0811 | 9.5920</item>
- <item>16 | 2.25 | 0.0742 0.0053 0.0794 | 8.8725</item>
- <item>29 | 2.00 | 0.0750 0.0024 0.0773 | 3.3283</item>
- <item>30 | 2.00 | 0.0689 0.0048 0.0737 | 3.1221</item>
- <item>31 | 2.00 | 0.0669 0.0057 0.0726 | 2.9160</item>
- <item>43 | 1.75 | 0.0656 0.0033 0.0690 | 1.5785</item>
- <item>44 | 1.75 | 0.0616 0.0054 0.0670 | 1.5194</item>
- <item>45 | 1.75 | 0.0602 0.0062 0.0664 | 1.4626</item>
- <item>57 | 1.50 | 0.0586 0.0045 0.0631 | 1.0900</item>
- <item>58 | 1.50 | 0.0556 0.0064 0.0620 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 145s</item>
- <item>Prepare output 10s</item>
- <item>155s</item>
- <item>Jacobian determinant (RMS): 0.013 0.047 0.068 0.092 0.115 | 0.119704</item>
- <item>Template Matching: 0.087 0.223 0.201 0.181 0.167 | 0.166762</item>
- <item>Write result maps: 31s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 29s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 41s</item>
- <item>90s</item>
- <item>Create initial surface 79s</item>
- <item>Topology correction: 75s</item>
- <item>Surface refinement: 88s</item>
- <item>Reduction of surface collisions with optimization: 60s</item>
- <item>Spherical mapping with areal smoothing 85s</item>
- <item>Spherical registration 305s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 39s</item>
- <item>85s</item>
- <item>Create initial surface 76s</item>
- <item>Topology correction: 71s</item>
- <item>Surface refinement: 90s</item>
- <item>Reduction of surface collisions with optimization: 56s</item>
- <item>Spherical mapping with areal smoothing 68s</item>
- <item>Spherical registration 291s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4641 0.6105 mm</item>
- <item>Surface intensity / position RMSE: 0.0677 / 0.0649</item>
- <item>Euler number / defect number / defect size: 18.0 / 11.5 / 0.40%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/surf/lh.thickness.sub-0027271_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/surf/rh.thickness.sub-0027271_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/sub-0027271_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1607s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 8s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 28s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 19s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 16s</item>
- <item>ROI estimation of 'anatomy3' atlas 22s</item>
- <item>ROI estimation of 'julichbrain' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 7s</item>
- <item>304s</item>
- <item>Quality check: 10s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/report/catreport_sub-0027271_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 44 minute(s) and 53 second(s).</item>
- <item>Image Quality Rating (IQR): 83.31% (B-)</item>
- <item>GM volume (GMV): 49.58% (627.09 / 1264.89 ml)</item>
- <item>GM thickness (GMT): 2.46 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_612028/ds/UWM/sub-0027271/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|