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- <opts>
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- </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>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <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>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
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- </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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- <thick_limit>5</thick_limit>
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- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
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- <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>
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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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- <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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- <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>
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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/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>
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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/Schaefer2018_100Parcels_17Networks_order.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_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>
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- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_4013887/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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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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- <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>
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- <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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- <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>
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- <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>
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- <VT>15</VT>
- <NV>17</NV>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
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- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
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- </shootingtpms>
- <templates>
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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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- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>514</SurfaceEulerNumber>
- <SurfaceDefectArea>18.5652606140235</SurfaceDefectArea>
- <SurfaceDefectNumber>180.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.12520632147789</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.202752932906151</SurfacePositionRMSE>
- <res_vx_vol>[1.33000183105469 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1.12084861758235</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[0 26.3899993896484 172.755004882812 305.153015136719]</tissue_mn>
- <tissue_mnr>[0 0.0864811986684799 0.566125810146332 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[6.19120150337892 63.5141056941043 40.5824562398594 30.9492025820535]</tissue_std>
- <tissue_stdr>[0.0202888417989016 0.208138555288315 0.132990509271622 0.101421914994717]</tissue_stdr>
- <contrast>105.753372192383</contrast>
- <contrastr>0.346558511257172</contrastr>
- <res_ECR>0.586025834083557</res_ECR>
- <NCR>0.274236708879471</NCR>
- <ICR>0.6479412317276</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>3.8878870010376</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[1.89584374427795 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>2.88495564460754</contrastr>
- <NCR>4.26782512664795</NCR>
- <ICR>2.06681847572327</ICR>
- <SurfaceEulerNumber>10.5</SurfaceEulerNumber>
- <SurfaceDefectArea>5.64131515350587</SurfaceDefectArea>
- <SurfaceDefectNumber>10.025</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>2.50412654876709</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>4.05505847930908</SurfacePositionRMSE>
- <SIQR>3.90708387601627</SIQR>
- <IQR>3.91644006954343</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>20231031-042455</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>514</SurfaceEulerNumber>
- <SurfaceDefectArea>18.5652606140235</SurfaceDefectArea>
- <SurfaceDefectNumber>180.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.12520632147789</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.202752932906151</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>514</EC_abs>
- <defect_size>18.5652606140235</defect_size>
- <vol_abs_CGW>[91.4223450980392 741.994180392157 435.982984313725 0 0]</vol_abs_CGW>
- <vol_abs_WMH>2.88562745098039</vol_abs_WMH>
- <vol_rel_WMH>0.00227322243997567</vol_rel_WMH>
- <surf_TSA>1706.47315021521</surf_TSA>
- <vol_TIV>1269.39950980392</vol_TIV>
- <vol_rel_CGW>[0.072020151569273 0.584523764710425 0.343456083720302 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.4962720472687 0.905750803075072]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.59112048149109 1.17866224075078 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.17441116900413 0.432821124694798 0.220966871827567;2.41297175751294 0.309598664310247 0.411870724111719;3.40527956611125 0.396079799009462 0.367162404060715]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.187082077667845 0.0791026833996917 0.298206278026906;4.5167290011153 0.250807185231511 0.701793721973094]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.39573061827229</vol_TIV>
- <vol_rel_CGW>[0.5 8.34776876275908 4.01824863003415 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.22732224399757</vol_rel_WMH>
- <surf_TSA>8.51000430626427</surf_TSA>
- <SQR>6.8289731127348</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.467397715702313]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00202015787363052 0.00160617008805275 0.236031472682953]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[906.597254901961 346.513898039216 81.1770549019608 761.570925490196 2613.07806666667 7164.11178823529]</SPMvols0>
- <SPMvols1>[755.020749019608 304.500078431373 44.2272078431373 646.578890196078 2049.20540392157 7349.372]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[11.2236995697021 171.88020324707 284.203308105469]</T3th>
- <Tth>
- <T3th>[-44.1839218139648 -44.1839218139648 -16.480110168457 11.2236995697021 171.88020324707 284.203308105469 420.693115234375 956.933654785156]</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>[0.0172223914414644 0.0588016659021378 0.0677430406212807 0 0]</dtc>
- <ll>[0.12189039434133 0 0.12189039434133 0;0.210427475433533 0.0174979190437161 0.227925394477249 3731.39624023438;0.210427475433533 0.0174979190437161 0.227925394477249 3731.39624023438]</ll>
- <rmsdtc>[0.0462179593741894 0.0995637178421021 0.131091058254242]</rmsdtc>
- <rmsgdt>[0.0353957116603851 0.0734153911471367 0.102220356464386]</rmsgdt>
- <rmsdt>0.131091058254242</rmsdt>
- <dt>0.0677430406212807</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>[0.00855641905218363 0.0217054653912783 0.0505711771547794 0.0592174045741558 0.0743569806218147 0.0869572460651398]</dtc>
- <ll>[0.130752586607371 0 0.130752586607371 0;0.100080993080993 0.010549733541921 0.110630726622914 16200.4345703125;0.224302112337991 0.0386894531032899 0.262991565441281 27845.263671875;0.217266608054368 0.040541533844197 0.257808141898565 43714.80078125;0.197719010256935 0.0450196265419272 0.242738636798862 78755.21875;0.197719010256935 0.0450196265419272 0.242738636798862 78755.21875]</ll>
- <rmsdtc>[0.0130530064925551 0.0329441353678703 0.0726150274276733 0.129837900400162 0.182599902153015 0.195609822869301]</rmsdtc>
- <rmsgdt>[0.00592414988204837 0.0187203157693148 0.0472497120499611 0.0885860025882721 0.127486288547516 0.138604268431664]</rmsgdt>
- <rmsdt>0.195609822869301</rmsdt>
- <dt>0.0869572460651398</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025025/ses-1/sub-0025025_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 36s</item>
- <item>Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>28s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 10s</item>
- <item>Use initial fine affine registration. 9s</item>
- <item>Use previous fine affine registration. 46s</item>
- <item>SPM preprocessing 1 (estimate 2): 55s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 13s</item>
- <item>Update Segmentation 14s</item>
- <item>Update Skull-Stripping 32s</item>
- <item>Update probability maps 7s</item>
- <item>66s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 21s</item>
- <item>Fast Optimized Shooting registration 27s</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) 10s</item>
- <item>Estimate local tissue thresholds (WM) 14s</item>
- <item>Estimate local tissue thresholds (GM) 21s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 37s</item>
- <item>89s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 5s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 5s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 18s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 3s</item>
- <item>45s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 26s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.35 0.05,0.69 0.08,0.97 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 3s</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>8s</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 | 0.1308 0.0000 0.1308 | 32.0000</item>
- <item>2 | 2.50 | 0.1129 0.0043 0.1172 | 29.4886</item>
- <item>3 | 2.50 | 0.1072 0.0066 0.1138 | 26.9772</item>
- <item>4 | 2.50 | 0.1042 0.0078 0.1120 | 24.6107</item>
- <item>5 | 2.50 | 0.1022 0.0086 0.1108 | 22.6548</item>
- <item>6 | 2.50 | 0.1007 0.0090 0.1097 | 20.6989</item>
- <item>7 | 2.50 | 0.0996 0.0092 0.1089 | 18.9688</item>
- <item>8 | 2.50 | 0.0984 0.0095 0.1079 | 17.4455</item>
- <item>9 | 2.50 | 0.0973 0.0095 0.1068 | 15.9223</item>
- <item>10 | 2.50 | 0.0962 0.0096 0.1058 | 14.6627</item>
- <item>11 | 2.50 | 0.0952 0.0097 0.1049 | 13.4764</item>
- <item>12 | 2.50 | 0.0943 0.0096 0.1038 | 12.3015</item>
- <item>13 | 2.50 | 0.0933 0.0097 0.1029 | 11.3776</item>
- <item>14 | 2.50 | 0.0924 0.0096 0.1020 | 10.4537</item>
- <item>15 | 2.25 | 0.1001 0.0105 0.1106 | 9.5920</item>
- <item>16 | 2.25 | 0.0941 0.0133 0.1075 | 8.8725</item>
- <item>17 | 2.25 | 0.0921 0.0137 0.1058 | 8.1530</item>
- <item>18 | 2.25 | 0.0906 0.0137 0.1043 | 7.5234</item>
- <item>19 | 2.25 | 0.0894 0.0136 0.1030 | 6.9630</item>
- <item>20 | 2.25 | 0.0882 0.0134 0.1016 | 6.4027</item>
- <item>21 | 2.25 | 0.0872 0.0133 0.1004 | 5.9447</item>
- <item>22 | 2.25 | 0.0862 0.0131 0.0993 | 5.5083</item>
- <item>23 | 2.25 | 0.0853 0.0128 0.0981 | 5.0803</item>
- <item>24 | 2.25 | 0.0844 0.0127 0.0971 | 4.7404</item>
- <item>25 | 2.25 | 0.0836 0.0124 0.0960 | 4.4005</item>
- <item>26 | 2.25 | 0.0828 0.0122 0.0950 | 4.0868</item>
- <item>27 | 2.25 | 0.0820 0.0121 0.0941 | 3.8221</item>
- <item>28 | 2.25 | 0.0813 0.0118 0.0931 | 3.5574</item>
- <item>29 | 2.00 | 0.0858 0.0119 0.0977 | 3.3283</item>
- <item>30 | 2.00 | 0.0822 0.0135 0.0957 | 3.1221</item>
- <item>31 | 2.00 | 0.0809 0.0137 0.0946 | 2.9160</item>
- <item>32 | 2.00 | 0.0799 0.0138 0.0937 | 2.7495</item>
- <item>33 | 2.00 | 0.0791 0.0137 0.0928 | 2.5890</item>
- <item>34 | 2.00 | 0.0783 0.0135 0.0919 | 2.4330</item>
- <item>35 | 2.00 | 0.0776 0.0135 0.0911 | 2.3080</item>
- <item>36 | 2.00 | 0.0770 0.0133 0.0903 | 2.1830</item>
- <item>37 | 2.00 | 0.0764 0.0132 0.0896 | 2.0688</item>
- <item>38 | 2.00 | 0.0758 0.0131 0.0889 | 1.9714</item>
- <item>39 | 2.00 | 0.0753 0.0130 0.0882 | 1.8740</item>
- <item>40 | 2.00 | 0.0748 0.0129 0.0877 | 1.7907</item>
- <item>43 | 1.75 | 0.0757 0.0115 0.0871 | 1.5785</item>
- <item>44 | 1.75 | 0.0724 0.0135 0.0859 | 1.5194</item>
- <item>57 | 1.50 | 0.0727 0.0103 0.0830 | 1.0900</item>
- <item>58 | 1.50 | 0.0675 0.0139 0.0815 | 1.0730</item>
- <item>59 | 1.50 | 0.0659 0.0150 0.0809 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 189s</item>
- <item>Prepare output 8s</item>
- <item>197s</item>
- <item>Jacobian determinant (RMS): 0.013 0.033 0.073 0.130 0.183 | 0.195610</item>
- <item>Template Matching: 0.131 0.100 0.224 0.217 0.198 | 0.197719</item>
- <item>Write result maps: 43s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 21s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 37s</item>
- <item>76s</item>
- <item>Create initial surface 73s</item>
- <item>Topology correction: 87s</item>
- <item>Surface refinement: 93s</item>
- <item>Reduction of surface collisions with optimization: 114s</item>
- <item>Spherical mapping with areal smoothing 78s</item>
- <item>Spherical registration 255s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 19s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 37s</item>
- <item>75s</item>
- <item>Create initial surface 75s</item>
- <item>Topology correction: 97s</item>
- <item>Surface refinement: 83s</item>
- <item>Reduction of surface collisions with optimization: 110s</item>
- <item>Spherical mapping with areal smoothing 65s</item>
- <item>Spherical registration 261s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4962 0.9052 mm</item>
- <item>Surface intensity / position RMSE: 0.1252 / 0.2028</item>
- <item>Euler number / defect number / defect size: 514.0 / 180.5 / 18.57%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4013887/ds/NYU_2/sub-0025025/ses-1/surf/lh.thickness.sub-0025025_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4013887/ds/NYU_2/sub-0025025/ses-1/surf/rh.thickness.sub-0025025_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_4013887/ds/NYU_2/sub-0025025/ses-1/sub-0025025_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1623s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 24s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 17s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 14s</item>
- <item>ROI estimation of 'anatomy3' atlas 20s</item>
- <item>ROI estimation of 'julichbrain' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 44s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 65s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 7s</item>
- <item>280s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_4013887/ds/NYU_2/sub-0025025/ses-1/report/catreport_sub-0025025_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 45 minute(s) and 3 second(s).</item>
- <item>Image Quality Rating (IQR): 65.84% (D)</item>
- <item>GM volume (GMV): 58.45% (741.99 / 1269.40 ml)</item>
- <item>GM thickness (GMT): 2.50 0.91 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_4013887/ds/NYU_2/sub-0025025/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_4013887/ds/NYU_2/sub-0025025/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_4013887/ds/NYU_2/sub-0025025/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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