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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>
- <NCstr>-Inf</NCstr>
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- <WMHC>2</WMHC>
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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>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <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>
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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>
- <td>
- <item>csf</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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- <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>
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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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- <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>/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_3468819/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</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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- <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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- <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>
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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>
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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>
- <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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- <shootingtpm>
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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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- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>0.770385707834059</SurfaceDefectArea>
- <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0723013579845428</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.073592908680439</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>200.467987060547</res_BB>
- <tissue_mn>[13.8990001678467 102.013999938965 289.239990234375 449.381988525391]</tissue_mn>
- <tissue_mnr>[0.0309291444718838 0.227009549736977 0.643639504909515 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[9.62447040862132 47.749643721505 49.8357116959602 29.6947565836752]</tissue_std>
- <tissue_stdr>[0.0221006795763969 0.109647549688816 0.114437788724899 0.0681880936026573]</tissue_stdr>
- <contrast>161.681564331055</contrast>
- <contrastr>0.359786480665207</contrastr>
- <res_ECR>0.377348601818085</res_ECR>
- <NCR>0.137833207845688</NCR>
- <ICR>0.241501837968826</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.82320713996887</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>2.68653607368469</contrastr>
- <NCR>2.30969285964966</NCR>
- <ICR>1.05878436565399</ICR>
- <SurfaceEulerNumber>2.22448979591837</SurfaceEulerNumber>
- <SurfaceDefectArea>1.19259642695851</SurfaceDefectArea>
- <SurfaceDefectNumber>1.925</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.44602715969086</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.47185814380646</SurfacePositionRMSE>
- <SIQR>2.53411006646122</SIQR>
- <IQR>2.19197724539911</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>20231031-021923</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>0.770385707834059</SurfaceDefectArea>
- <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0723013579845428</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.073592908680439</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>26</EC_abs>
- <defect_size>0.770385707834059</defect_size>
- <vol_abs_CGW>[202.678631372549 860.142623529412 586.795788235294 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.287976470588235</vol_abs_WMH>
- <vol_rel_WMH>0.000174571711529216</vol_rel_WMH>
- <surf_TSA>2233.67586822962</surf_TSA>
- <vol_TIV>1649.61704313725</vol_TIV>
- <vol_rel_CGW>[0.122864050305332 0.521419578627525 0.355716371067142 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.74925255886401 0.638839162277986]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.76677536964417 0.786898511200666 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.10498327654561 0.272732801372044 0.28337804347008;2.7761553220427 0.188213543111885 0.432238606979082;3.45429148229932 0.275857108249388 0.284383349550838]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.968678002883682 0.378292812735581 0.603045133224579;4.35072352472506 0.297965304766599 0.396954866775421]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.34891784005744</vol_TIV>
- <vol_rel_CGW>[0.5 7.21443208741964 4.23844057232655 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01745717115292</vol_rel_WMH>
- <surf_TSA>8.62394766128042</surf_TSA>
- <SQR>5.91011457976491</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.648 0.350010713884744]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0125182066112757 0.00081768975360319 0.32161346077919]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1001.92382745098 526.336184313725 350.842458823529 476.629403921569 1369.63783921569 6272.02974901961]</SPMvols0>
- <SPMvols1>[891.126839215686 498.854984313725 188.170933333333 391.776109803922 1047.23038823529 6354.52771372549]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[106.712799072266 300.073303222656 439.287811279297]</T3th>
- <Tth>
- <T3th>[-6.7315502166748 -6.73155069351196 9.91583347320557 106.712799072266 300.073303222656 439.287811279297 605.575317382812 1068.89001464844]</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>[0.0196774154901505 0.0704241544008255 0.0771817117929459 0 0]</dtc>
- <ll>[0.0821032026091687 0 0.0821032026091687 0;0.190809068988924 0.00968122310569736 0.200490292094621 2064.50146484375;0.190809068988924 0.00968122310569736 0.200490292094621 2064.50146484375]</ll>
- <rmsdtc>[0.0457785278558731 0.0924015045166016 0.101848915219307]</rmsdtc>
- <rmsgdt>[0.0333842411637306 0.041486281901598 0.0505460500717163]</rmsgdt>
- <rmsdt>0.101848915219307</rmsdt>
- <dt>0.0771817117929459</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>[0.00919950194656849 0.0341605469584465 0.0476840548217297 0.0550030246376991 0.0600121505558491 0.066808857023716]</dtc>
- <ll>[0.08261100389706 0 0.08261100389706 0;0.212107341269841 0.0142541380494505 0.226361479319292 7296.3369140625;0.189960337433585 0.0162646330233482 0.206224970456933 11705.8515625;0.171310598694022 0.0175216870430188 0.18883228573704 18893.14453125;0.15825738501606 0.0182422991260912 0.176499684142151 31912.220703125;0.15825738501606 0.0182422991260912 0.176499684142151 31912.220703125]</ll>
- <rmsdtc>[0.010910945944488 0.0400767512619495 0.059727631509304 0.0823859348893166 0.10361510515213 0.108120806515217]</rmsdtc>
- <rmsgdt>[0.00328363594599068 0.0126783167943358 0.0271152220666409 0.0460432581603527 0.0639917403459549 0.0684803500771523]</rmsgdt>
- <rmsdt>0.108120806515217</rmsdt>
- <dt>0.066808857023716</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025267/ses-1/sub-0025267_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 72s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>44s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 92s</item>
- <item>SPM preprocessing 1 (estimate 2): 87s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 24s</item>
- <item>Update Skull-Stripping 45s</item>
- <item>Update probability maps 9s</item>
- <item>97s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 37s</item>
- <item>Fast Optimized Shooting registration 40s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 19s</item>
- <item>Estimate local tissue thresholds (WM) 24s</item>
- <item>Estimate local tissue thresholds (GM) 38s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 47s</item>
- <item>139s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 18s</item>
- <item>Blood vessel detection 14s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 34s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 4s</item>
- <item>90s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 41s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 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>15s</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 | 0.0826 0.0000 0.0826 | 32.0000</item>
- <item>2 | 2.50 | 0.0798 0.0012 0.0810 | 29.4886</item>
- <item>3 | 2.50 | 0.0790 0.0019 0.0808 | 26.9772</item>
- <item>4 | 2.50 | 0.0786 0.0021 0.0807 | 24.6107</item>
- <item>5 | 2.50 | 0.0782 0.0023 0.0805 | 22.6548</item>
- <item>6 | 2.50 | 0.0779 0.0024 0.0803 | 20.6989</item>
- <item>7 | 2.50 | 0.0776 0.0025 0.0801 | 18.9688</item>
- <item>8 | 2.50 | 0.0773 0.0026 0.0799 | 17.4455</item>
- <item>9 | 2.50 | 0.0770 0.0027 0.0797 | 15.9223</item>
- <item>10 | 2.50 | 0.0766 0.0028 0.0794 | 14.6627</item>
- <item>11 | 2.50 | 0.0763 0.0029 0.0792 | 13.4764</item>
- <item>12 | 2.50 | 0.0760 0.0029 0.0789 | 12.3015</item>
- <item>13 | 2.50 | 0.0756 0.0030 0.0786 | 11.3776</item>
- <item>14 | 2.50 | 0.0753 0.0031 0.0784 | 10.4537</item>
- <item>15 | 2.25 | 0.0738 0.0032 0.0770 | 9.5920</item>
- <item>16 | 2.25 | 0.0707 0.0048 0.0755 | 8.8725</item>
- <item>29 | 2.00 | 0.0711 0.0021 0.0732 | 3.3283</item>
- <item>30 | 2.00 | 0.0652 0.0045 0.0697 | 3.1221</item>
- <item>31 | 2.00 | 0.0633 0.0054 0.0687 | 2.9160</item>
- <item>43 | 1.75 | 0.0622 0.0031 0.0653 | 1.5785</item>
- <item>44 | 1.75 | 0.0583 0.0051 0.0635 | 1.5194</item>
- <item>45 | 1.75 | 0.0571 0.0058 0.0629 | 1.4626</item>
- <item>57 | 1.50 | 0.0555 0.0043 0.0598 | 1.0900</item>
- <item>58 | 1.50 | 0.0528 0.0061 0.0588 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 175s</item>
- <item>Prepare output 14s</item>
- <item>189s</item>
- <item>Jacobian determinant (RMS): 0.011 0.040 0.060 0.082 0.104 | 0.108121</item>
- <item>Template Matching: 0.083 0.212 0.190 0.171 0.158 | 0.158257</item>
- <item>Write result maps: 50s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 56s</item>
- <item>CSF distance: 24s</item>
- <item>PBT2x thickness: 69s</item>
- <item>158s</item>
- <item>Create initial surface 117s</item>
- <item>Topology correction: 130s</item>
- <item>Surface refinement: 125s</item>
- <item>Reduction of surface collisions with optimization: 110s</item>
- <item>Spherical mapping with areal smoothing 126s</item>
- <item>Spherical registration 345s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 53s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 69s</item>
- <item>152s</item>
- <item>Create initial surface 115s</item>
- <item>Topology correction: 132s</item>
- <item>Surface refinement: 106s</item>
- <item>Reduction of surface collisions with optimization: 108s</item>
- <item>Spherical mapping with areal smoothing 135s</item>
- <item>Spherical registration 370s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.7494 0.6386 mm</item>
- <item>Surface intensity / position RMSE: 0.0723 / 0.0736</item>
- <item>Euler number / defect number / defect size: 26.0 / 18.5 / 0.77%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-1/surf/lh.thickness.sub-0025267_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-1/surf/rh.thickness.sub-0025267_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-1/sub-0025267_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 2361s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 31s</item>
- <item>ROI estimation of 'lpba40' atlas 9s</item>
- <item>ROI estimation of 'hammers' atlas 24s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 13s</item>
- <item>ROI estimation of 'mori' atlas 19s</item>
- <item>ROI estimation of 'anatomy3' atlas 26s</item>
- <item>ROI estimation of 'julichbrain' atlas 34s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 55s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 83s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 9s</item>
- <item>357s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-1/report/catreport_sub-0025267_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 64 minute(s) and 7 second(s).</item>
- <item>Image Quality Rating (IQR): 83.08% (B-)</item>
- <item>GM volume (GMV): 52.14% (860.14 / 1649.62 ml)</item>
- <item>GM thickness (GMT): 2.75 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3468819/ds/UPSM_1/sub-0025267/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|