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- <opts>
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- <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>
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- <regstr>0.5</regstr>
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- <SLC>0</SLC>
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- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
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- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
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- <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>
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- <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>
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- <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>
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- <item>csf</item>
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- <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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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.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/hammers.nii</td>
- <td>0</td>
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- <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/thalamus.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/suit.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/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>
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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>
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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>/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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- <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>
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- <item>gm</item>
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- <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>/var/lib/condor/execute/dir_2624533/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>
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- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </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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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.683872847670216</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0641895681619644</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0649109780788422</SurfacePositionRMSE>
- <res_vx_vol>[1.19999994591369 0.500000011229762 0.499999995090881]</res_vx_vol>
- <res_vx_voli>[0.800000042094898 0.799999970891906 0.799999979647467]</res_vx_voli>
- <res_RMS>0.804155846527586</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[22.7224998474121 53.6220016479492 223.369003295898 371.743988037109]</tissue_mn>
- <tissue_mnr>[0.0611240528523922 0.144244432449341 0.600867807865143 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[12.1485776001439 44.5620634776836 45.9628883367711 25.4220005711228]</tissue_std>
- <tissue_stdr>[0.0348075367510319 0.127677142620087 0.131690710783005 0.0728379264473915]</tissue_stdr>
- <contrast>129.482116699219</contrast>
- <contrastr>0.348309934139252</contrastr>
- <res_ECR>0.328054666519165</res_ECR>
- <NCR>0.127961203455925</NCR>
- <ICR>0</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.39999989182737 1.00000002245952 0.999999990181762]</res_vx_vol>
- <res_RMS>1.60831169305517</res_RMS>
- <res_ECR>2.57170748710632</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>2.85868430137634</contrastr>
- <NCR>2.16797590255737</NCR>
- <ICR>0.5</ICR>
- <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
- <SurfaceDefectArea>1.17096821191755</SurfaceDefectArea>
- <SurfaceDefectNumber>1.65</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.28379130363464</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.29821956157684</SurfacePositionRMSE>
- <SIQR>2.31162701165991</SIQR>
- <IQR>2.00997317663367</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>20231031-012020</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.683872847670216</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0641895681619644</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0649109780788422</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>16</EC_abs>
- <defect_size>0.683872847670216</defect_size>
- <vol_abs_CGW>[361.694064120804 818.103864718564 619.419913355723 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.17909583228113</vol_abs_WMH>
- <vol_rel_WMH>0.000655338005565018</vol_rel_WMH>
- <surf_TSA>2301.81660930224</surf_TSA>
- <vol_TIV>1799.21784219509</vol_TIV>
- <vol_rel_CGW>[0.201028500072858 0.454699728700143 0.344271771226999 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.5334057570478 0.605087289295386]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.54777383804321 0.739805518208473 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.91455542394621 0.254167027026058 0.270543337853555;2.54127008672053 0.174830590760047 0.434337966114413;3.16844769400257 0.25859046070782 0.295118696032031]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.842852610629468 0.370370836915957 0.569609507640068;4.07857148125327 0.345601440083531 0.430390492359932]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>3.99076814662072</vol_TIV>
- <vol_rel_CGW>[1.46028196969932 6.01615892062038 4.03289819014007 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0655338005565</vol_rel_WMH>
- <surf_TSA>8.62398542856565</surf_TSA>
- <SQR>4.94445278419486</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11796.4796174326 0.369183530695604]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00127825373783708 0.0010360071901232 0.0163464713841677]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1000.09909792918 530.116018836782 745.695506232299 506.009852345006 994.85679021274 8700.12309002988]</SPMvols0>
- <SPMvols1>[848.999657124298 504.0207966143 403.396895423114 478.804730587645 862.363965330662 8699.07011887095]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[76.3744964599609 230.743392944336 377.127105712891]</T3th>
- <Tth>
- <T3th>[-145.351974487305 -65.5328521728516 5.42082214355469 76.3744964599609 230.743392944336 377.127105712891 527.50341796875 983.198425292969]</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>[0.0236057788133621 0.0823138877749443 0.0914755761623383 0 0]</dtc>
- <ll>[0.090133325058539 0 0.090133325058539 0;0.208257063811853 0.0114089672734328 0.219666031085286 2432.939453125;0.208257063811853 0.0114089672734328 0.219666031085286 2432.939453125]</ll>
- <rmsdtc>[0.0538461096584797 0.107851602137089 0.119491659104824]</rmsdtc>
- <rmsgdt>[0.0387122482061386 0.0494151785969734 0.0609961226582527]</rmsgdt>
- <rmsdt>0.119491659104824</rmsdt>
- <dt>0.0914755761623383</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>[0.0106445224955678 0.0432585850358009 0.0525990016758442 0.0608414709568024 0.0677189752459526 0.0755017474293709]</dtc>
- <ll>[0.0889821913367274 0 0.0889821913367274 0;0.223704746642247 0.0171701312576313 0.240874877899878 8788.9609375;0.210319131993075 0.0178358235655373 0.228154955558612 12836.65625;0.190530876601637 0.0198348843247576 0.210365760926394 21387.400390625;0.172463833771686 0.0234343827760892 0.195898216547775 40995.0078125;0.172463833771686 0.0234343827760892 0.195898216547775 40995.0078125]</ll>
- <rmsdtc>[0.0123233459889889 0.043515894562006 0.0646342039108276 0.085698775947094 0.109191827476025 0.115663059055805]</rmsdtc>
- <rmsgdt>[0.00325429067015648 0.0124103603884578 0.0276069771498442 0.0477906353771687 0.0693241432309151 0.07431261241436]</rmsgdt>
- <rmsdt>0.115663059055805</rmsdt>
- <dt>0.0755017474293709</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026043/ses-1/sub-0026043_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 226s</item>
- <item>Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 9s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 4s</item>
- <item>Final correction 7s</item>
- <item>Final scaling 7s</item>
- <item>51s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 27s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 102s</item>
- <item>SPM preprocessing 1 (estimate 2): 38s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 23s</item>
- <item>Update Segmentation 28s</item>
- <item>Update Skull-Stripping 61s</item>
- <item>Update probability maps 12s</item>
- <item>124s</item>
- <item>Global intensity correction: 22s</item>
- <item>SANLM denoising after intensity normalization (medium): 50s</item>
- <item>Fast Optimized Shooting registration 31s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.04) 23s</item>
- <item>Estimate local tissue thresholds (WM) 26s</item>
- <item>Estimate local tissue thresholds (GM) 38s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 56s</item>
- <item>157s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 10s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 16s</item>
- <item>Blood vessel detection 16s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 32s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 6s</item>
- <item>95s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.37 0.05,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 6s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>16s</item>
- <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
- <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
- <item>1 | 2.50 | 0.0890 0.0000 0.0890 | 32.0000</item>
- <item>2 | 2.50 | 0.0857 0.0014 0.0871 | 29.4886</item>
- <item>3 | 2.50 | 0.0848 0.0021 0.0868 | 26.9772</item>
- <item>4 | 2.50 | 0.0843 0.0023 0.0866 | 24.6107</item>
- <item>5 | 2.50 | 0.0839 0.0025 0.0864 | 22.6548</item>
- <item>6 | 2.50 | 0.0836 0.0026 0.0862 | 20.6989</item>
- <item>7 | 2.50 | 0.0833 0.0027 0.0860 | 18.9688</item>
- <item>8 | 2.50 | 0.0829 0.0028 0.0858 | 17.4455</item>
- <item>9 | 2.50 | 0.0826 0.0029 0.0855 | 15.9223</item>
- <item>10 | 2.50 | 0.0822 0.0030 0.0852 | 14.6627</item>
- <item>11 | 2.50 | 0.0818 0.0031 0.0850 | 13.4764</item>
- <item>12 | 2.50 | 0.0815 0.0032 0.0846 | 12.3015</item>
- <item>13 | 2.50 | 0.0811 0.0033 0.0844 | 11.3776</item>
- <item>14 | 2.50 | 0.0807 0.0033 0.0841 | 10.4537</item>
- <item>15 | 2.25 | 0.0803 0.0034 0.0837 | 9.5920</item>
- <item>16 | 2.25 | 0.0771 0.0049 0.0821 | 8.8725</item>
- <item>17 | 2.25 | 0.0759 0.0054 0.0814 | 8.1530</item>
- <item>18 | 2.25 | 0.0752 0.0056 0.0808 | 7.5234</item>
- <item>19 | 2.25 | 0.0746 0.0057 0.0803 | 6.9630</item>
- <item>29 | 2.00 | 0.0768 0.0029 0.0797 | 3.3283</item>
- <item>30 | 2.00 | 0.0718 0.0051 0.0769 | 3.1221</item>
- <item>31 | 2.00 | 0.0701 0.0059 0.0761 | 2.9160</item>
- <item>43 | 1.75 | 0.0695 0.0033 0.0729 | 1.5785</item>
- <item>44 | 1.75 | 0.0650 0.0058 0.0708 | 1.5194</item>
- <item>45 | 1.75 | 0.0635 0.0066 0.0701 | 1.4626</item>
- <item>57 | 1.50 | 0.0621 0.0048 0.0669 | 1.0900</item>
- <item>58 | 1.50 | 0.0586 0.0071 0.0657 | 1.0730</item>
- <item>59 | 1.50 | 0.0575 0.0078 0.0653 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 115s</item>
- <item>Prepare output 11s</item>
- <item>126s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.065 0.086 0.109 | 0.115663</item>
- <item>Template Matching: 0.089 0.224 0.210 0.191 0.172 | 0.172464</item>
- <item>Write result maps: 157s</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: 14s</item>
- <item>PBT2x thickness: 36s</item>
- <item>86s</item>
- <item>Create initial surface 65s</item>
- <item>Topology correction: 75s</item>
- <item>Surface refinement: 76s</item>
- <item>Reduction of surface collisions with optimization: 58s</item>
- <item>Spherical mapping with areal smoothing 68s</item>
- <item>Spherical registration 185s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 34s</item>
- <item>78s</item>
- <item>Create initial surface 62s</item>
- <item>Topology correction: 74s</item>
- <item>Surface refinement: 68s</item>
- <item>Reduction of surface collisions with optimization: 57s</item>
- <item>Spherical mapping with areal smoothing 84s</item>
- <item>Spherical registration 218s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5335 0.6049 mm</item>
- <item>Surface intensity / position RMSE: 0.0642 / 0.0649</item>
- <item>Euler number / defect number / defect size: 16.0 / 13.0 / 0.68%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/surf/lh.thickness.sub-0026043_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/surf/rh.thickness.sub-0026043_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/sub-0026043_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1374s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 45s</item>
- <item>ROI estimation of 'lpba40' atlas 13s</item>
- <item>ROI estimation of 'hammers' atlas 32s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 11s</item>
- <item>ROI estimation of 'aal3' atlas 18s</item>
- <item>ROI estimation of 'mori' atlas 27s</item>
- <item>ROI estimation of 'anatomy3' atlas 39s</item>
- <item>ROI estimation of 'julichbrain' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 22s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 38s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 127s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s</item>
- <item>Write results 11s</item>
- <item>539s</item>
- <item>Quality check: 40s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/report/catreport_sub-0026043_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 55 minute(s) and 8 second(s).</item>
- <item>Image Quality Rating (IQR): 84.90% (B)</item>
- <item>GM volume (GMV): 45.47% (818.10 / 1799.22 ml)</item>
- <item>GM thickness (GMT): 2.53 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2624533/ds/Utah_1/sub-0026043/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|