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- <F>/var/lib/condor/execute/dir_399/ds/sub-35/sub-35_acq-highres_T1w.nii</F>
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- <fnames>..r_399/ds/sub-35/sub-35_acq-highres_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
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- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
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- <fwhm>1</fwhm>
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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>
- <BVCstr>0.5</BVCstr>
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- <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_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>24</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>
- <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>
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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>
- <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>
- <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/lpba40.nii</td>
- <td>0</td>
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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/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>
- <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/ibsr.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/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>
- <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_400Parcels_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_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <satlas>
- <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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- <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>
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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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- <CB>3</CB>
- <BG>5</BG>
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- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
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- <PH>25</PH>
- <LE>27</LE>
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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>
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- </shootingtpms>
- <templates>
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- </templates>
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- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>6</SurfaceEulerNumber>
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- <res_BB>0</res_BB>
- <tissue_mn>[1.22099995613098 59.6070213317871 142.307266235352 195.951141357422]</tissue_mn>
- <tissue_mnr>[0.00623114453628659 0.304193288087845 0.726238489151001 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[21.9119318158252 21.3253409009903 17.885273279779 9.54292122371175]</tissue_std>
- <tissue_stdr>[0.112524598836899 0.109512269496918 0.0918464511632919 0.0490058735013008]</tissue_stdr>
- <contrast>53.9802322387695</contrast>
- <contrastr>0.275478005409241</contrastr>
- <NCR>0.112666442990303</NCR>
- <ICR>0.177780523896217</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999998247978 1.99999996766515 2.00000001894021]</res_vx_vol>
- <res_RMS>1.99999998969505</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[5.48201417922974 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>3.95116329193115</contrastr>
- <NCR>1.94841289520264</NCR>
- <ICR>0.900745332241058</ICR>
- <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0319601072715</SurfaceDefectArea>
- <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.17042660713196</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.11832880973816</SurfacePositionRMSE>
- <IQR>1.97538398377245</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>20220712-145100</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>6</SurfaceEulerNumber>
- <SurfaceDefectArea>0.12784042908601</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0585213303565979</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0559164434671402</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>6</EC_abs>
- <defect_size>0.12784042908601</defect_size>
- <vol_abs_CGW>[312.402484405177 653.723414970114 481.703039926003 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.23167447151165</vol_abs_WMH>
- <vol_rel_WMH>0.000850704415471927</vol_rel_WMH>
- <surf_TSA>1893.86536178187</surf_TSA>
- <vol_TIV>1447.82893930129</vol_TIV>
- <vol_rel_CGW>[0.215773062635382 0.451519787472679 0.332707149891939 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.59606331817722 0.63753207630255]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.59388399124146 0.773647711738426 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.98185386572639 0.256809105718803 0.301289426701051;2.62337839662798 0.183764178446021 0.425986907359651;3.29854983122498 0.278062254687803 0.272723665939298]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.923061091544665 0.319675685949459 0.555730757859466;4.26353834171473 0.352283776173493 0.444269242140534]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.05430789842273</vol_TIV>
- <vol_rel_CGW>[1.72509092376764 5.9590479071961 3.82520024949604 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08507044154719</vol_rel_WMH>
- <surf_TSA>8.6123899387531</surf_TSA>
- <SQR>4.89047552527049</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.506336847941081 2506 206 6211.71990398281 0.340062493314474]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00546531612053514 0 0.0969317406415939]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[772.368838732456 434.740464915463 444.393095987915 556.514657207983 1660.27311308865 9230.72335615771]</SPMvols0>
- <SPMvols1>[685.815947305704 407.581889289224 304.271665050118 428.529461186992 1092.6802287741 9664.05100935239]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[66.4077987670898 145.567199707031 191.107894897461]</T3th>
- <Tth>
- <T3th>[0 0 1.49924921989441 66.4077987670898 145.567199707031 191.107894897461 253.457946777344 469.865875244141]</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>[0.0227065328508615 0.0777254477143288 0.0862221196293831 0 0]</dtc>
- <ll>[0.0884461023178803 0 0.0884461023178803 0;0.206791633889884 0.011726277501357 0.218517911391241 2500.60522460938;0.206791633889884 0.011726277501357 0.218517911391241 2500.60522460938]</ll>
- <rmsdtc>[0.0472088418900967 0.102866001427174 0.114516526460648]</rmsdtc>
- <rmsgdt>[0.0330692529678345 0.0486887320876122 0.0599715150892735]</rmsgdt>
- <rmsdt>0.114516526460648</rmsdt>
- <dt>0.0862221196293831</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>[0.0105905700474977 0.0407038405537605 0.0528545454144478 0.0623652376234531 0.0691297352313995 0.0776060819625854]</dtc>
- <ll>[0.0878853791426921 0 0.0878853791426921 0;0.224408318070818 0.0164878624847375 0.240896180555556 8439.724609375;0.207228724823263 0.0184312901592929 0.225660014982556 13265.220703125;0.185196212667119 0.0207591767777518 0.205955389444871 22384.0390625;0.166602023719627 0.0236847811555186 0.190286804875145 41433.04296875;0.166602023719627 0.0236847811555186 0.190286804875145 41433.04296875]</ll>
- <rmsdtc>[0.0122900530695915 0.0428654290735722 0.0648193955421448 0.0900253728032112 0.114705838263035 0.121315412223339]</rmsdtc>
- <rmsgdt>[0.0033164257183671 0.0130538512021303 0.0293078422546387 0.0505858920514584 0.0690455585718155 0.0747214257717133]</rmsgdt>
- <rmsdt>0.121315412223339</rmsdt>
- <dt>0.0776060819625854</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_399/ds/sub-35/sub-35_acq-highres_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 57s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 10s</item>
- <item>Estimate background 9s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 5s</item>
- <item>Final correction 7s</item>
- <item>Final scaling 7s</item>
- <item>56s</item>
- <item>Correct center-of-mass 9s</item>
- <item>Affine registration 15s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 7s</item>
- <item>Use initial fine affine registration. 6s</item>
- <item>Use previous fine affine registration. 86s</item>
- <item>SPM preprocessing 1 (estimate 2): 93s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 26s</item>
- <item>Update Segmentation 27s</item>
- <item>Update Skull-Stripping 60s</item>
- <item>Update probability maps 13s</item>
- <item>125s</item>
- <item>Global intensity correction: 25s</item>
- <item>SANLM denoising after intensity normalization (medium): 13s</item>
- <item>Fast Optimized Shooting registration 51s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.04) 20s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 31s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 40s</item>
- <item>128s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 12s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 12s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.16) 31s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 5s</item>
- <item>Final corrections 7s</item>
- <item>91s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 53s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05]</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 | 0.0879 0.0000 0.0879 | 32.0000</item>
- <item>2 | 2.50 | 0.0851 0.0012 0.0863 | 29.4886</item>
- <item>3 | 2.50 | 0.0842 0.0019 0.0861 | 26.9772</item>
- <item>4 | 2.50 | 0.0838 0.0021 0.0860 | 24.6107</item>
- <item>5 | 2.50 | 0.0835 0.0023 0.0858 | 22.6548</item>
- <item>6 | 2.50 | 0.0832 0.0024 0.0856 | 20.6989</item>
- <item>7 | 2.50 | 0.0830 0.0025 0.0854 | 18.9688</item>
- <item>8 | 2.50 | 0.0826 0.0026 0.0852 | 17.4455</item>
- <item>9 | 2.50 | 0.0823 0.0027 0.0850 | 15.9223</item>
- <item>10 | 2.50 | 0.0820 0.0028 0.0848 | 14.6627</item>
- <item>11 | 2.50 | 0.0817 0.0029 0.0845 | 13.4764</item>
- <item>12 | 2.50 | 0.0814 0.0029 0.0843 | 12.3015</item>
- <item>13 | 2.50 | 0.0810 0.0030 0.0840 | 11.3776</item>
- <item>14 | 2.50 | 0.0807 0.0031 0.0838 | 10.4537</item>
- <item>15 | 2.25 | 0.0800 0.0032 0.0832 | 9.5920</item>
- <item>16 | 2.25 | 0.0768 0.0047 0.0815 | 8.8725</item>
- <item>17 | 2.25 | 0.0756 0.0053 0.0808 | 8.1530</item>
- <item>18 | 2.25 | 0.0748 0.0055 0.0803 | 7.5234</item>
- <item>29 | 2.00 | 0.0769 0.0026 0.0795 | 3.3283</item>
- <item>30 | 2.00 | 0.0711 0.0052 0.0762 | 3.1221</item>
- <item>31 | 2.00 | 0.0691 0.0061 0.0752 | 2.9160</item>
- <item>43 | 1.75 | 0.0681 0.0035 0.0716 | 1.5785</item>
- <item>44 | 1.75 | 0.0633 0.0060 0.0694 | 1.5194</item>
- <item>45 | 1.75 | 0.0617 0.0069 0.0687 | 1.4626</item>
- <item>57 | 1.50 | 0.0600 0.0050 0.0650 | 1.0900</item>
- <item>58 | 1.50 | 0.0566 0.0072 0.0639 | 1.0730</item>
- <item>59 | 1.50 | 0.0555 0.0079 0.0634 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 274s</item>
- <item>Prepare output 14s</item>
- <item>287s</item>
- <item>Jacobian determinant (RMS): 0.012 0.043 0.065 0.090 0.115 | 0.121315</item>
- <item>Template Matching: 0.088 0.224 0.207 0.185 0.167 | 0.166602</item>
- <item>Write result maps: 38s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 59s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 62s</item>
- <item>150s</item>
- <item>Create initial surface 109s</item>
- <item>Topology correction: 121s</item>
- <item>Surface refinement: 112s</item>
- <item>Reduction of surface collisions with optimization: 100s</item>
- <item>Spherical mapping with areal smoothing 109s</item>
- <item>Spherical registration 321s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 60s</item>
- <item>CSF distance: 24s</item>
- <item>PBT2x thickness: 62s</item>
- <item>154s</item>
- <item>Create initial surface 108s</item>
- <item>Topology correction: 121s</item>
- <item>Surface refinement: 109s</item>
- <item>Reduction of surface collisions with optimization: 92s</item>
- <item>Spherical mapping with areal smoothing 107s</item>
- <item>Spherical registration 302s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5961 0.6375 mm</item>
- <item>Surface intensity / position RMSE: 0.0585 / 0.0559</item>
- <item>Euler number / defect number / defect size: 6.0 / 10.5 / 0.13%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_399/ds/sub-35/surf/lh.thickness.sub-35_acq-highres_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_399/ds/sub-35/surf/rh.thickness.sub-35_acq-highres_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_399/ds/sub-35/sub-35_acq-highres_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 2136s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 18s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 64s</item>
- <item>ROI estimation of 'lpba40' atlas 18s</item>
- <item>ROI estimation of 'hammers' atlas 45s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 16s</item>
- <item>ROI estimation of 'aal3' atlas 26s</item>
- <item>ROI estimation of 'mori' atlas 39s</item>
- <item>ROI estimation of 'anatomy3' atlas 58s</item>
- <item>ROI estimation of 'julichbrain' atlas 76s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 120s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 183s</item>
- <item>Write results 184s</item>
- <item>732s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_399/ds/sub-35/report/catreport_sub-35_acq-highres_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 69 minute(s) and 29 second(s).</item>
- <item>Image Quality Rating (IQR): 85.25% (B)</item>
- <item>GM volume (GMV): 45.15% (653.72 / 1447.83 ml)</item>
- <item>GM thickness (GMT): 2.60 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_399/ds/sub-35/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_399/ds/sub-35/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_399/ds/sub-35/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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