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- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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- <biasfwhm>60</biasfwhm>
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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>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
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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>
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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>
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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>[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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- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>/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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- <tr>
- <td>/var/lib/condor/execute/dir_3298722/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>
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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>
- </LAB>
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- <shootingtpm>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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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>28</SurfaceEulerNumber>
- <SurfaceDefectArea>1.11444266595778</SurfaceDefectArea>
- <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0827829837799072</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0833011344075203</SurfacePositionRMSE>
- <res_vx_vol>[1.20000002609716 0.5 0.499999990983826]</res_vx_vol>
- <res_vx_voli>[0.800000058178973 0.800000011920929 0.799999998645488]</res_vx_voli>
- <res_RMS>0.80415588323347</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[23.753999710083 58.3950004577637 218.162002563477 390.118988037109]</tissue_mn>
- <tissue_mnr>[0.0608891136944294 0.149685099720955 0.559219121932983 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[12.7987543321113 40.3408152642626 41.2654489768408 28.4055912389982]</tissue_std>
- <tissue_stdr>[0.0349344350397587 0.110110998153687 0.112634807825089 0.0775335878133774]</tissue_stdr>
- <contrast>132.430328369141</contrast>
- <contrastr>0.339461386203766</contrastr>
- <res_ECR>0.315145671367645</res_ECR>
- <NCR>0.142765164375305</NCR>
- <ICR>0.271155416965485</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.40000005219432 1 0.999999981967652]</res_vx_vol>
- <res_RMS>1.60831176646694</res_RMS>
- <res_ECR>2.50584506988525</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>2.99141263961792</contrastr>
- <NCR>2.38049340248108</NCR>
- <ICR>1.1323299407959</ICR>
- <SurfaceEulerNumber>2.3265306122449</SurfaceEulerNumber>
- <SurfaceDefectArea>1.27861066648944</SurfaceDefectArea>
- <SurfaceDefectNumber>1.875</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.65565967559814</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.66602265834808</SurfacePositionRMSE>
- <SIQR>2.33274243720486</SIQR>
- <IQR>2.19454906791566</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>20231031-035613</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>28</SurfaceEulerNumber>
- <SurfaceDefectArea>1.11444266595778</SurfaceDefectArea>
- <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0827829837799072</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0833011344075203</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>28</EC_abs>
- <defect_size>1.11444266595778</defect_size>
- <vol_abs_CGW>[191.856582196372 845.505777314599 553.916315018596 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.445923928515094</vol_abs_WMH>
- <vol_rel_WMH>0.000280229940646269</vol_rel_WMH>
- <surf_TSA>2137.57937095419</surf_TSA>
- <vol_TIV>1591.27867452957</vol_TIV>
- <vol_rel_CGW>[0.120567556938505 0.531337339491813 0.348095103569682 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.77998490797298 0.67730563829483]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.79809045791626 0.905597417362478 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.12444006078538 0.296403557201613 0.296071757586456;2.83555663081375 0.202773970269685 0.44114807725194;3.58866216314833 0.310764105441207 0.262780165161604]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.822715148543015 0.409445157503338 0.676582997624212;4.49543266530922 0.237674038474821 0.323417002375788]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.82371086625633</vol_TIV>
- <vol_rel_CGW>[0.5 7.39255279259722 4.10156436008768 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.02802299406463</vol_rel_WMH>
- <surf_TSA>8.6237156991313</surf_TSA>
- <SQR>6.05213301298875</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[2.54313151041667e-08 1 1 11796.4797438273 0.446605352234288]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00103972433134913 0.00085578381549567 0.0267585664987564]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[982.501293777057 480.264944046469 553.18136405348 741.408301639911 1024.10303212844 8651.22180167329]</SPMvols0>
- <SPMvols1>[835.813943760195 457.149846718972 260.649259480395 513.580529905413 921.833711842218 8808.11006387654]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[79.4141998291016 228.568893432617 393.459899902344]</T3th>
- <Tth>
- <T3th>[-202.596374511719 -65.798454284668 6.8078727722168 79.4141998291016 228.568893432617 393.459899902344 550.482788085938 1076.34814453125]</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>[0.0203094780445099 0.0711958780884743 0.0784605666995049 0 0]</dtc>
- <ll>[0.0855798129798794 0 0.0855798129798794 0;0.201077629538143 0.0105713664555178 0.211648995993661 2254.32275390625;0.201077629538143 0.0105713664555178 0.211648995993661 2254.32275390625]</ll>
- <rmsdtc>[0.0467391051352024 0.0955567583441734 0.106124691665173]</rmsdtc>
- <rmsgdt>[0.0337788239121437 0.0454261898994446 0.0560846924781799]</rmsgdt>
- <rmsdt>0.106124691665173</rmsdt>
- <dt>0.0784605666995049</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>[0.00876867678016424 0.0313349366188049 0.0448966138064861 0.05445346981287 0.0621191076934338 0.0702362433075905]</dtc>
- <ll>[0.082722953251127 0 0.082722953251127 0;0.215791132478632 0.0141677903693529 0.229958922847985 7252.1376953125;0.19458354088163 0.0175666892190904 0.212150230100721 12642.95703125;0.174389512224188 0.0201457495476559 0.194535261771844 21722.59765625;0.157127985318 0.0236173142477533 0.180745299565754 41315.01953125;0.157127985318 0.0236173142477533 0.180745299565754 41315.01953125]</ll>
- <rmsdtc>[0.0106401275843382 0.0379381962120533 0.0594131164252758 0.0885393619537354 0.117469139397144 0.125344812870026]</rmsdtc>
- <rmsgdt>[0.00336707010865211 0.0132800377905369 0.0302568599581718 0.0538893789052963 0.0761585831642151 0.0829758197069168]</rmsgdt>
- <rmsdt>0.125344812870026</rmsdt>
- <dt>0.0702362433075905</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026022/ses-1/sub-0026022_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 322s</item>
- <item>Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 3s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 15s</item>
- <item>Estimate background 13s</item>
- <item>Initial correction 14s</item>
- <item>Refine background 7s</item>
- <item>Final correction 12s</item>
- <item>Final scaling 11s</item>
- <item>86s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 20s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 154s</item>
- <item>SPM preprocessing 1 (estimate 2): 78s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 40s</item>
- <item>Update Segmentation 43s</item>
- <item>Update Skull-Stripping 101s</item>
- <item>Update probability maps 21s</item>
- <item>205s</item>
- <item>Global intensity correction: 38s</item>
- <item>SANLM denoising after intensity normalization (medium): 67s</item>
- <item>Fast Optimized Shooting registration 59s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 9s</item>
- <item>Prepare partitions 5s</item>
- <item>Prepare segments (LASmod = 1.00) 35s</item>
- <item>Estimate local tissue thresholds (WM) 51s</item>
- <item>Estimate local tissue thresholds (GM) 75s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 103s</item>
- <item>286s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 16s</item>
- <item>Major structures 8s</item>
- <item>Ventricle detection 43s</item>
- <item>Blood vessel detection 29s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 67s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 5s</item>
- <item>Side alignment 10s</item>
- <item>Final corrections 10s</item>
- <item>188s</item>
- <item>Blood vessel correction (BVCstr=0.50): 4s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 68s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.07,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 11s</item>
- <item>Level 1 cleanup (brain masking) 6s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
- <item>27s</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 | 0.0827 0.0000 0.0827 | 32.0000</item>
- <item>2 | 2.50 | 0.0798 0.0013 0.0811 | 29.4886</item>
- <item>3 | 2.50 | 0.0790 0.0019 0.0809 | 26.9772</item>
- <item>4 | 2.50 | 0.0786 0.0021 0.0807 | 24.6107</item>
- <item>5 | 2.50 | 0.0783 0.0023 0.0805 | 22.6548</item>
- <item>6 | 2.50 | 0.0780 0.0024 0.0803 | 20.6989</item>
- <item>7 | 2.50 | 0.0777 0.0024 0.0802 | 18.9688</item>
- <item>8 | 2.50 | 0.0774 0.0025 0.0800 | 17.4455</item>
- <item>9 | 2.50 | 0.0771 0.0026 0.0797 | 15.9223</item>
- <item>10 | 2.50 | 0.0768 0.0027 0.0795 | 14.6627</item>
- <item>11 | 2.50 | 0.0765 0.0028 0.0792 | 13.4764</item>
- <item>12 | 2.50 | 0.0762 0.0028 0.0790 | 12.3015</item>
- <item>13 | 2.50 | 0.0758 0.0029 0.0787 | 11.3776</item>
- <item>14 | 2.50 | 0.0755 0.0030 0.0785 | 10.4537</item>
- <item>15 | 2.25 | 0.0754 0.0030 0.0784 | 9.5920</item>
- <item>16 | 2.25 | 0.0719 0.0047 0.0767 | 8.8725</item>
- <item>29 | 2.00 | 0.0736 0.0021 0.0757 | 3.3283</item>
- <item>30 | 2.00 | 0.0669 0.0049 0.0718 | 3.1221</item>
- <item>31 | 2.00 | 0.0649 0.0059 0.0707 | 2.9160</item>
- <item>43 | 1.75 | 0.0643 0.0033 0.0677 | 1.5785</item>
- <item>44 | 1.75 | 0.0596 0.0059 0.0655 | 1.5194</item>
- <item>45 | 1.75 | 0.0581 0.0067 0.0648 | 1.4626</item>
- <item>57 | 1.50 | 0.0569 0.0049 0.0618 | 1.0900</item>
- <item>58 | 1.50 | 0.0535 0.0072 0.0606 | 1.0730</item>
- <item>59 | 1.50 | 0.0524 0.0079 0.0602 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 197s</item>
- <item>Prepare output 21s</item>
- <item>218s</item>
- <item>Jacobian determinant (RMS): 0.011 0.038 0.059 0.089 0.117 | 0.125345</item>
- <item>Template Matching: 0.083 0.216 0.195 0.174 0.157 | 0.157128</item>
- <item>Write result maps: 240s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 45s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 65s</item>
- <item>140s</item>
- <item>Create initial surface 108s</item>
- <item>Topology correction: 120s</item>
- <item>Surface refinement: 142s</item>
- <item>Reduction of surface collisions with optimization: 96s</item>
- <item>Spherical mapping with areal smoothing 115s</item>
- <item>Spherical registration 338s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 44s</item>
- <item>CSF distance: 23s</item>
- <item>PBT2x thickness: 66s</item>
- <item>141s</item>
- <item>Create initial surface 111s</item>
- <item>Topology correction: 123s</item>
- <item>Surface refinement: 108s</item>
- <item>Reduction of surface collisions with optimization: 99s</item>
- <item>Spherical mapping with areal smoothing 131s</item>
- <item>Spherical registration 347s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.7800 0.6771 mm</item>
- <item>Surface intensity / position RMSE: 0.0828 / 0.0833</item>
- <item>Euler number / defect number / defect size: 28.0 / 17.5 / 1.11%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3298722/ds/Utah_1/sub-0026022/ses-1/surf/lh.thickness.sub-0026022_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3298722/ds/Utah_1/sub-0026022/ses-1/surf/rh.thickness.sub-0026022_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3298722/ds/Utah_1/sub-0026022/ses-1/sub-0026022_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 2310s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 19s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 68s</item>
- <item>ROI estimation of 'lpba40' atlas 20s</item>
- <item>ROI estimation of 'hammers' atlas 50s</item>
- <item>ROI estimation of 'thalamus' atlas 4s</item>
- <item>ROI estimation of 'ibsr' atlas 17s</item>
- <item>ROI estimation of 'aal3' atlas 27s</item>
- <item>ROI estimation of 'mori' atlas 40s</item>
- <item>ROI estimation of 'anatomy3' atlas 57s</item>
- <item>ROI estimation of 'julichbrain' atlas 76s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 122s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 15s</item>
- <item>Write results 17s</item>
- <item>782s</item>
- <item>Quality check: 63s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3298722/ds/Utah_1/sub-0026022/ses-1/report/catreport_sub-0026022_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 89 minute(s) and 8 second(s).</item>
- <item>Image Quality Rating (IQR): 83.05% (B-)</item>
- <item>GM volume (GMV): 53.13% (845.51 / 1591.28 ml)</item>
- <item>GM thickness (GMT): 2.78 0.68 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3298722/ds/Utah_1/sub-0026022/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3298722/ds/Utah_1/sub-0026022/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3298722/ds/Utah_1/sub-0026022/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|