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- <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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- <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>
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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>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
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- <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>
- <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>
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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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- <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>
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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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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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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_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_2614792/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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- <satlas>
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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>
- </LAB>
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- <shooting>
- <shootingtpm>
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- <pbtmethod>pbt2x</pbtmethod>
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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_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>
- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.34083570711041</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0714113414287567</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0664176493883133</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>180.336029052734</res_BB>
- <tissue_mn>[157.615997314453 474.760986328125 1466.61901855469 2357.19506835938]</tissue_mn>
- <tissue_mnr>[0.0668659135699272 0.201409295201302 0.622188210487366 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[67.7673547019258 249.794703477988 255.105852537821 168.879531370396]</tissue_std>
- <tissue_stdr>[0.030809236690402 0.113564774394035 0.115979395806789 0.0767781138420105]</tissue_stdr>
- <contrast>830.572692871094</contrast>
- <contrastr>0.352356374263763</contrastr>
- <res_ECR>0.377788424491882</res_ECR>
- <NCR>0.134414449334145</NCR>
- <ICR>0.303283482789993</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.82545113563538</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>2.79798769950867</contrastr>
- <NCR>2.26061511039734</NCR>
- <ICR>1.21201264858246</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0852089267776</SurfaceDefectArea>
- <SurfaceDefectNumber>1.7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.42822682857513</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.32835292816162</SurfacePositionRMSE>
- <SIQR>2.52771306180499</SIQR>
- <IQR>2.15724369246005</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>20231030-235958</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.34083570711041</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0714113414287567</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0664176493883133</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>0.34083570711041</defect_size>
- <vol_abs_CGW>[219.05042745098 718.07968627451 473.13608627451 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.667560784313725</vol_abs_WMH>
- <vol_rel_WMH>0.000473357997457307</vol_rel_WMH>
- <surf_TSA>1958.87563153669</surf_TSA>
- <vol_TIV>1410.2662</vol_TIV>
- <vol_rel_CGW>[0.155325588495974 0.509180242903439 0.335494168600587 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.53005797711501 0.606338055005801]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.50770735740662 0.698541391948084 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95181161695199 0.240261172609647 0.301573625928085;2.53760208766982 0.17280696535538 0.430358817119834;3.19756891827007 0.253826647564069 0.268067556952082]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.963426445826179 0.33374110482256 0.538939103441979;4.08580764558056 0.332482035245042 0.461060896558021]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.0025106191275</vol_TIV>
- <vol_rel_CGW>[0.639468184194928 6.99461643145544 3.8752544648094 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04733579974573</vol_rel_WMH>
- <surf_TSA>8.61931657056849</surf_TSA>
- <SQR>5.72627839080862</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10223.616 0.488107841045581]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00169429276138544 0.00134891190100461 0.148948237299919]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[895.924611764706 409.363996078431 369.931662745098 553.3662 1047.43405098039 7490.04516862745]</SPMvols0>
- <SPMvols1>[780.301580392157 381.082529411765 213.885109803922 490.007803921569 822.445478431373 7535.92041176471]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[570.890930175781 1573.93273925781 2367.45434570312]</T3th>
- <Tth>
- <T3th>[-29.2204704284668 -29.2204666137695 58.7474517822266 570.890930175781 1573.93273925781 2367.45434570312 3265.73608398438 11634.404296875]</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>[0.0210419371724129 0.0700911432504654 0.077399767935276 0 0]</dtc>
- <ll>[0.0851592101684424 0 0.0851592101684424 0;0.203538214602247 0.00995204256934707 0.213490257171594 2122.25317382812;0.203538214602247 0.00995204256934707 0.213490257171594 2122.25317382812]</ll>
- <rmsdtc>[0.0448942966759205 0.0940428301692009 0.105430409312248]</rmsdtc>
- <rmsgdt>[0.0318975150585175 0.0462285727262497 0.0575461350381374]</rmsgdt>
- <rmsdt>0.105430409312248</rmsdt>
- <dt>0.077399767935276</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>[0.00989942718297243 0.0397832542657852 0.049034908413887 0.057569082826376 0.0649294331669807 0.0725919157266617]</dtc>
- <ll>[0.0871487730509267 0 0.0871487730509267 0;0.223345604395604 0.0162038614163614 0.239549465811966 8294.3515625;0.21022721154434 0.0170461983621574 0.227273409906497 12268.353515625;0.190840225726904 0.0188617398369799 0.209701965563884 20338.0859375;0.174443029794444 0.0221961705270463 0.19663920032149 38828.9375;0.174443029794444 0.0221961705270463 0.19663920032149 38828.9375]</ll>
- <rmsdtc>[0.0115375751629472 0.0404052324593067 0.061579804867506 0.0841663181781769 0.108531668782234 0.115411438047886]</rmsdtc>
- <rmsgdt>[0.00317922583781183 0.0123561387881637 0.0279133133590221 0.0489778332412243 0.0690239071846008 0.0750153437256813]</rmsgdt>
- <rmsdt>0.115411438047886</rmsdt>
- <dt>0.0725919157266617</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027267/ses-1/sub-0027267_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 53s</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 5s</item>
- <item>33s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 77s</item>
- <item>SPM preprocessing 1 (estimate 2): 52s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 38s</item>
- <item>Update probability maps 8s</item>
- <item>77s</item>
- <item>Global intensity correction: 14s</item>
- <item>SANLM denoising after intensity normalization (medium): 26s</item>
- <item>Fast Optimized Shooting registration 32s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 13s</item>
- <item>Estimate local tissue thresholds (WM) 16s</item>
- <item>Estimate local tissue thresholds (GM) 25s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 38s</item>
- <item>102s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 9s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 23s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>67s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 31s</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) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>10s</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 | 0.0871 0.0000 0.0871 | 32.0000</item>
- <item>2 | 2.50 | 0.0844 0.0012 0.0857 | 29.4886</item>
- <item>3 | 2.50 | 0.0837 0.0018 0.0855 | 26.9772</item>
- <item>4 | 2.50 | 0.0833 0.0020 0.0853 | 24.6107</item>
- <item>5 | 2.50 | 0.0830 0.0022 0.0852 | 22.6548</item>
- <item>6 | 2.50 | 0.0827 0.0023 0.0850 | 20.6989</item>
- <item>7 | 2.50 | 0.0824 0.0024 0.0848 | 18.9688</item>
- <item>8 | 2.50 | 0.0821 0.0025 0.0846 | 17.4455</item>
- <item>9 | 2.50 | 0.0818 0.0026 0.0844 | 15.9223</item>
- <item>10 | 2.50 | 0.0815 0.0027 0.0842 | 14.6627</item>
- <item>11 | 2.50 | 0.0812 0.0027 0.0839 | 13.4764</item>
- <item>12 | 2.50 | 0.0809 0.0028 0.0837 | 12.3015</item>
- <item>13 | 2.50 | 0.0805 0.0029 0.0834 | 11.3776</item>
- <item>14 | 2.50 | 0.0802 0.0030 0.0832 | 10.4537</item>
- <item>15 | 2.25 | 0.0801 0.0031 0.0832 | 9.5920</item>
- <item>16 | 2.25 | 0.0770 0.0046 0.0815 | 8.8725</item>
- <item>17 | 2.25 | 0.0758 0.0051 0.0809 | 8.1530</item>
- <item>18 | 2.25 | 0.0750 0.0053 0.0803 | 7.5234</item>
- <item>19 | 2.25 | 0.0744 0.0054 0.0798 | 6.9630</item>
- <item>29 | 2.00 | 0.0764 0.0028 0.0792 | 3.3283</item>
- <item>30 | 2.00 | 0.0717 0.0049 0.0766 | 3.1221</item>
- <item>31 | 2.00 | 0.0701 0.0057 0.0758 | 2.9160</item>
- <item>43 | 1.75 | 0.0693 0.0032 0.0725 | 1.5785</item>
- <item>44 | 1.75 | 0.0650 0.0055 0.0705 | 1.5194</item>
- <item>45 | 1.75 | 0.0636 0.0063 0.0699 | 1.4626</item>
- <item>57 | 1.50 | 0.0625 0.0046 0.0671 | 1.0900</item>
- <item>58 | 1.50 | 0.0592 0.0067 0.0660 | 1.0730</item>
- <item>59 | 1.50 | 0.0581 0.0074 0.0655 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 175s</item>
- <item>Prepare output 12s</item>
- <item>187s</item>
- <item>Jacobian determinant (RMS): 0.012 0.040 0.062 0.084 0.109 | 0.115411</item>
- <item>Template Matching: 0.087 0.223 0.210 0.191 0.174 | 0.174443</item>
- <item>Write result maps: 34s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 33s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 47s</item>
- <item>102s</item>
- <item>Create initial surface 89s</item>
- <item>Topology correction: 119s</item>
- <item>Surface refinement: 72s</item>
- <item>Reduction of surface collisions with optimization: 70s</item>
- <item>Spherical mapping with areal smoothing 80s</item>
- <item>Spherical registration 282s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 44s</item>
- <item>92s</item>
- <item>Create initial surface 84s</item>
- <item>Topology correction: 90s</item>
- <item>Surface refinement: 106s</item>
- <item>Reduction of surface collisions with optimization: 68s</item>
- <item>Spherical mapping with areal smoothing 80s</item>
- <item>Spherical registration 287s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5301 0.6063 mm</item>
- <item>Surface intensity / position RMSE: 0.0714 / 0.0664</item>
- <item>Euler number / defect number / defect size: 14.0 / 14.0 / 0.34%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-1/surf/lh.thickness.sub-0027267_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-1/surf/rh.thickness.sub-0027267_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-1/sub-0027267_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1714s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 26s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 19s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 11s</item>
- <item>ROI estimation of 'mori' atlas 17s</item>
- <item>ROI estimation of 'anatomy3' atlas 26s</item>
- <item>ROI estimation of 'julichbrain' atlas 37s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 65s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 127s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 12s</item>
- <item>Write results 14s</item>
- <item>407s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-1/report/catreport_sub-0027267_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 50 minute(s) and 56 second(s).</item>
- <item>Image Quality Rating (IQR): 83.43% (B)</item>
- <item>GM volume (GMV): 50.92% (718.08 / 1410.27 ml)</item>
- <item>GM thickness (GMT): 2.53 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2614792/ds/UWM/sub-0027267/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|