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- <file>sub-sc034_T1w</file>
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- <Fm>/var/lib/condor/execute/dir_18373/ds/sub-sc034/mri/msub-sc034_T1w.nii</Fm>
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- <fnames>..73/ds/sub-sc034/sub-sc034_T1w</fnames>
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- <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>
- <affreg>mni</affreg>
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- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
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- <WMHC>2</WMHC>
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- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>32</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>
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- </darteltpm>
- <shootingtpm>
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- </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>
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- </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>
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- <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>
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- <tr>
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- <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/lpba40.nii</td>
- <td>0</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <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/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <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>
- </td>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </td>
- <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>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- <item>wm</item>
- </td>
- <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>
- <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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- </td>
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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>
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- <td>[false]</td>
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- <tr>
- <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>
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- <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>
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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>
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- </satlas>
- <LAB>
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- <CT>1</CT>
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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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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
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- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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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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- <SurfaceEulerNumber>26</SurfaceEulerNumber>
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- <tissue_mnr>[0 0.11054015904665 0.513988971710205 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2629.73495334353 34742.5322282887 43129.069944239 32528.0599437776]</tissue_std>
- <tissue_stdr>[0.00766822881996632 0.101308189332485 0.125763088464737 0.0948508530855179]</tissue_stdr>
- <contrast>115272.4921875</contrast>
- <contrastr>0.336131155490875</contrastr>
- <NCR>0.164444878697395</NCR>
- <ICR>0.308282554149628</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000002151778 2.00000003093298 1.99999998195355]</res_vx_vol>
- <res_RMS>2.0000000114681</res_RMS>
- <res_BB>0.5</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>3.0413658618927</contrastr>
- <NCR>2.69171524047852</NCR>
- <ICR>1.22441112995148</ICR>
- <SurfaceEulerNumber>2.22448979591837</SurfaceEulerNumber>
- <SurfaceDefectArea>1.19832005235189</SurfaceDefectArea>
- <SurfaceDefectNumber>1.65</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.44115030765533</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.63258290290833</SurfacePositionRMSE>
- <IQR>2.4958749687803</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>1980</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>20220711-184459</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>0.793280209407548</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0720575153827667</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.081629142165184</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>26</EC_abs>
- <defect_size>0.793280209407548</defect_size>
- <vol_abs_CGW>[211.79285615341 723.334758843845 496.75239644685 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.732588253187508</vol_abs_WMH>
- <vol_rel_WMH>0.000511626845358826</vol_rel_WMH>
- <surf_TSA>2010.5018041672</surf_TSA>
- <vol_TIV>1431.8800114441</vol_TIV>
- <vol_rel_CGW>[0.147912432927818 0.505164366471136 0.346923200601045 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.48665682387272 0.597315029498268]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.47756719589233 0.729833237741957 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92855122201758 0.238820892863752 0.299627596173443;2.5081754104187 0.167487376893098 0.438195169249202;3.14584120756978 0.257959915498191 0.262177234577356]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.863685595975279 0.348857773274289 0.554717332588246;4.0870039810124 0.357914759325462 0.445282667411754]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.02417577244407</vol_TIV>
- <vol_rel_CGW>[0.506329614364556 6.92249221392127 4.08051725217394 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05116268453588</vol_rel_WMH>
- <surf_TSA>8.62181688245642</surf_TSA>
- <SQR>5.67122358084046</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.700769255050505 2093 743 3791.85206522803 0.50914895744057]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.218980386853218]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[882.026684288506 435.044614547487 360.795248028072 1013.08536984254 4211.5277930622 6689.34993985725]</SPMvols0>
- <SPMvols1>[780.029089640362 411.010547293791 187.18372614057 102.020445629093 26.0570869109514 11165.837794293]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[46881.390625 198265 348300.8125]</T3th>
- <Tth>
- <T3th>[0 0 20487.515625 46881.390625 198265 348300.8125 499010.53125 1013530.0625]</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>[0.0208769906312227 0.0753695666790009 0.0831234902143478 0 0]</dtc>
- <ll>[0.0822708111564938 0 0.0822708111564938 0;0.19037438583832 0.0100642761834959 0.200438662021816 2146.18676757812;0.19037438583832 0.0100642761834959 0.200438662021816 2146.18676757812]</ll>
- <rmsdtc>[0.0463985837996006 0.0989909172058105 0.109447941184044]</rmsdtc>
- <rmsgdt>[0.0332718528807163 0.0456381738185883 0.0560233257710934]</rmsgdt>
- <rmsdt>0.109447941184044</rmsdt>
- <dt>0.0831234902143478</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>[0.00998143013566732 0.0368355847895145 0.0516239628195763 0.0592791512608528 0.065299317240715 0.0737194716930389]</dtc>
- <ll>[0.0841303852846253 0 0.0841303852846253 0;0.217659004884005 0.014241701007326 0.231900705891331 7289.970703125;0.196221739563881 0.0168290460715536 0.213050785635435 12112.06640625;0.176592704577324 0.0184945688854482 0.195087273462772 19942.17578125;0.160377025820403 0.0212141780060971 0.1815912038265 37111.0859375;0.160377025820403 0.0212141780060971 0.1815912038265 37111.0859375]</ll>
- <rmsdtc>[0.0117681501433253 0.0427582673728466 0.0640469864010811 0.090363398194313 0.114416375756264 0.121063493192196]</rmsdtc>
- <rmsgdt>[0.00333579885773361 0.0131437135860324 0.0289975050836802 0.0499116592109203 0.0682492405176163 0.0736644119024277]</rmsgdt>
- <rmsdt>0.121063493192196</rmsdt>
- <dt>0.0737194716930389</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./execute/dir_18373/ds/sub-sc034/sub-sc034_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 26s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 6s</item>
- <item>38s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 77s</item>
- <item>SPM preprocessing 1 (estimate 2): 55s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 17s</item>
- <item>Update Segmentation 18s</item>
- <item>Update Skull-Stripping 41s</item>
- <item>Update probability maps 8s</item>
- <item>85s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 8s</item>
- <item>Fast Optimized Shooting registration 34s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 14s</item>
- <item>Estimate local tissue thresholds (WM) 19s</item>
- <item>Estimate local tissue thresholds (GM) 24s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 9s</item>
- <item>75s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 18s</item>
- <item>Blood vessel detection 9s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 25s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 5s</item>
- <item>72s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.99 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>11s</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 | 0.0841 0.0000 0.0841 | 32.0000</item>
- <item>2 | 2.50 | 0.0811 0.0013 0.0824 | 29.4886</item>
- <item>3 | 2.50 | 0.0802 0.0019 0.0822 | 26.9772</item>
- <item>4 | 2.50 | 0.0798 0.0022 0.0820 | 24.6107</item>
- <item>5 | 2.50 | 0.0795 0.0024 0.0818 | 22.6548</item>
- <item>6 | 2.50 | 0.0792 0.0025 0.0816 | 20.6989</item>
- <item>7 | 2.50 | 0.0789 0.0026 0.0814 | 18.9688</item>
- <item>8 | 2.50 | 0.0785 0.0027 0.0812 | 17.4455</item>
- <item>9 | 2.50 | 0.0782 0.0027 0.0810 | 15.9223</item>
- <item>10 | 2.50 | 0.0779 0.0029 0.0807 | 14.6627</item>
- <item>11 | 2.50 | 0.0775 0.0029 0.0805 | 13.4764</item>
- <item>12 | 2.50 | 0.0772 0.0030 0.0802 | 12.3015</item>
- <item>13 | 2.50 | 0.0768 0.0031 0.0800 | 11.3776</item>
- <item>14 | 2.50 | 0.0765 0.0032 0.0797 | 10.4537</item>
- <item>15 | 2.25 | 0.0755 0.0033 0.0788 | 9.5920</item>
- <item>16 | 2.25 | 0.0726 0.0047 0.0773 | 8.8725</item>
- <item>29 | 2.00 | 0.0737 0.0021 0.0758 | 3.3283</item>
- <item>30 | 2.00 | 0.0675 0.0046 0.0721 | 3.1221</item>
- <item>31 | 2.00 | 0.0654 0.0056 0.0710 | 2.9160</item>
- <item>43 | 1.75 | 0.0644 0.0032 0.0676 | 1.5785</item>
- <item>44 | 1.75 | 0.0602 0.0054 0.0656 | 1.5194</item>
- <item>45 | 1.75 | 0.0589 0.0062 0.0650 | 1.4626</item>
- <item>57 | 1.50 | 0.0575 0.0045 0.0620 | 1.0900</item>
- <item>58 | 1.50 | 0.0544 0.0064 0.0609 | 1.0730</item>
- <item>59 | 1.50 | 0.0535 0.0071 0.0605 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 160s</item>
- <item>Prepare output 10s</item>
- <item>170s</item>
- <item>Jacobian determinant (RMS): 0.012 0.043 0.064 0.090 0.114 | 0.121063</item>
- <item>Template Matching: 0.084 0.218 0.196 0.177 0.160 | 0.160377</item>
- <item>Write result maps: 24s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 41s</item>
- <item>90s</item>
- <item>Create initial surface 79s</item>
- <item>Topology correction: 94s</item>
- <item>Surface refinement: 84s</item>
- <item>Reduction of surface collisions with optimization: 74s</item>
- <item>Spherical mapping with areal smoothing 95s</item>
- <item>Spherical registration 306s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 26s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 44s</item>
- <item>91s</item>
- <item>Create initial surface 84s</item>
- <item>Topology correction: 97s</item>
- <item>Surface refinement: 84s</item>
- <item>Reduction of surface collisions with optimization: 69s</item>
- <item>Spherical mapping with areal smoothing 90s</item>
- <item>Spherical registration 297s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4867 0.5968 mm</item>
- <item>Surface intensity / position RMSE: 0.0721 / 0.0816</item>
- <item>Euler number / defect number / defect size: 26.0 / 13.0 / 0.79%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_18373/ds/sub-sc034/surf/lh.thickness.sub-sc034_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_18373/ds/sub-sc034/surf/rh.thickness.sub-sc034_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_18373/ds/sub-sc034/sub-sc034_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1728s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 33s</item>
- <item>ROI estimation of 'lpba40' atlas 9s</item>
- <item>ROI estimation of 'hammers' atlas 22s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 8s</item>
- <item>ROI estimation of 'aal3' atlas 13s</item>
- <item>ROI estimation of 'mori' atlas 20s</item>
- <item>ROI estimation of 'anatomy3' atlas 28s</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 26s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s</item>
- <item>Write results 89s</item>
- <item>370s</item>
- <item>Quality check: 5s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_18373/ds/sub-sc034/report/catreport_sub-sc034_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 48 minute(s) and 41 second(s).</item>
- <item>Image Quality Rating (IQR): 80.04% (B-)</item>
- <item>GM volume (GMV): 50.52% (723.33 / 1431.88 ml)</item>
- <item>GM thickness (GMT): 2.49 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_18373/ds/sub-sc034/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_18373/ds/sub-sc034/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_18373/ds/sub-sc034/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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