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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>
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- <vox>1.5</vox>
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- <shootingsurf>Template_T1</shootingsurf>
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- <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>
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- <reduce_mesh>1</reduce_mesh>
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- <thick_limit>5</thick_limit>
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- <scale_cortex>0.7</scale_cortex>
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- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
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- <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>
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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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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
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- <item>csf</item>
- <item>gm</item>
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- <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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- <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>
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- <item>gm</item>
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- <td>/var/lib/condor/execute/dir_2613068/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>
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- <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>
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- <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>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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- </darteltpms>
- <shootingtpms>
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- </shootingtpms>
- <templates>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
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- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>34</SurfaceEulerNumber>
- <SurfaceDefectArea>1.23242918051378</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0655081123113632</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0707311928272247</SurfacePositionRMSE>
- <res_vx_vol>[0.9375 0.9375 1]</res_vx_vol>
- <res_vx_voli>[0.9375 0.9375 1]</res_vx_voli>
- <res_RMS>0.958786124916988</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 8.09899997711182 44.2529983520508 85.6190032958984]</tissue_mn>
- <tissue_mnr>[0 0.0945934876799583 0.516859531402588 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[0.224109757362772 8.64153985589799 10.9931719003201 7.73523257961591]</tissue_std>
- <tissue_stdr>[0.00261752353981137 0.100930161774158 0.128396406769753 0.0903448089957237]</tissue_stdr>
- <contrast>28.8283672332764</contrast>
- <contrastr>0.336705237627029</contrastr>
- <res_ECR>0.326269209384918</res_ECR>
- <NCR>0.209219679236412</NCR>
- <ICR>0.279004693031311</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.875 1.875 2]</res_vx_vol>
- <res_RMS>1.91757224983398</res_RMS>
- <res_ECR>2.56259775161743</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[2.33525977824126 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.03275465965271</contrastr>
- <NCR>3.334477186203</NCR>
- <ICR>1.1517972946167</ICR>
- <SurfaceEulerNumber>2.63265306122449</SurfaceEulerNumber>
- <SurfaceDefectArea>1.30810729512844</SurfaceDefectArea>
- <SurfaceDefectNumber>1.775</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.31016230583191</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.41462385654449</SurfacePositionRMSE>
- <SIQR>2.95254890577178</SIQR>
- <IQR>3.06227725700618</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>20231031-000940</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>34</SurfaceEulerNumber>
- <SurfaceDefectArea>1.23242918051378</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0655081123113632</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0707311928272247</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>34</EC_abs>
- <defect_size>1.23242918051378</defect_size>
- <vol_abs_CGW>[258.222208180147 781.60283203125 570.897477022059 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.40983111213235</vol_abs_WMH>
- <vol_rel_WMH>0.000875278700737263</vol_rel_WMH>
- <surf_TSA>2180.79130975461</surf_TSA>
- <vol_TIV>1610.72251723346</vol_TIV>
- <vol_rel_CGW>[0.160314520606358 0.485249832710922 0.35443564668272 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.52066346493039 0.606790843084317]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.50470924377441 0.75216103895757 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95672119361276 0.239800336461036 0.308130667247708;2.53573279128968 0.16952441539232 0.415807675332004;3.1749848514761 0.265703096691162 0.276061657420288]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.879714589947324 0.360487779456434 0.529946613279947;4.13726931307944 0.370016038379038 0.470053386720053]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.98780517209389</vol_TIV>
- <vol_rel_CGW>[0.72906825801648 6.56483176564156 4.21543905680173 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08752787007373</vol_rel_WMH>
- <surf_TSA>8.62386502060024</surf_TSA>
- <SQR>5.38764775731785</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 12672 0.474192661803997]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00115325464867055 0.00110657163895667 0.0599382035434246]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[987.970560661765 496.566838235294 359.006897977941 702.538376608456 1337.73438419118 9475.65928883272]</SPMvols0>
- <SPMvols1>[873.6183984375 469.902390854779 191.105497472426 521.650508961397 1058.30541590074 9558.24958869485]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[10.1096000671387 48.4776000976562 85.6567001342773]</T3th>
- <Tth>
- <T3th>[-0.985180020332336 -0.98518443107605 0.243551641702652 10.1096000671387 48.4776000976562 85.6567001342773 123.430252075195 193.331832885742]</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>[0.018953550606966 0.0708661824464798 0.0780470743775368 0 0]</dtc>
- <ll>[0.0819971054828181 0 0.0819971054828181 0;0.195777975496839 0.0103181722212811 0.20609614771812 2200.32958984375;0.195777975496839 0.0103181722212811 0.20609614771812 2200.32958984375]</ll>
- <rmsdtc>[0.0434360429644585 0.0936079472303391 0.105048760771751]</rmsdtc>
- <rmsgdt>[0.0313739143311977 0.0450172275304794 0.056214764714241]</rmsgdt>
- <rmsdt>0.105048760771751</rmsdt>
- <dt>0.0780470743775368</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>[0.00937068741768599 0.0382352955639362 0.0495629720389843 0.0578194111585617 0.0645908564329147 0.0728772059082985]</dtc>
- <ll>[0.0852216933964144 0 0.0852216933964144 0;0.223803373015873 0.0158146396138584 0.239618012629731 8095.11865234375;0.209278394517529 0.0176704647245183 0.226948859242048 12717.6455078125;0.187916320047261 0.0204324043034828 0.208348724350744 22031.689453125;0.169519870346351 0.024178381057168 0.193698251403519 42296.5234375;0.169519870346351 0.024178381057168 0.193698251403519 42296.5234375]</ll>
- <rmsdtc>[0.0109319956973195 0.0400182120501995 0.0620555803179741 0.0867396146059036 0.112708374857903 0.120730556547642]</rmsdtc>
- <rmsgdt>[0.00322562200017273 0.0129224993288517 0.0299785528331995 0.0526296533644199 0.0737964734435081 0.0799274295568466]</rmsgdt>
- <rmsdt>0.120730556547642</rmsdt>
- <dt>0.0728772059082985</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025361/ses-1/sub-0025361_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 41s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 9s</item>
- <item>Refine background 4s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>47s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 99s</item>
- <item>SPM preprocessing 1 (estimate 2): 82s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 24s</item>
- <item>Update Skull-Stripping 52s</item>
- <item>Update probability maps 11s</item>
- <item>108s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 32s</item>
- <item>Fast Optimized Shooting registration 36s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.07) 17s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 31s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 50s</item>
- <item>132s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 9s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 19s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 32s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>87s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 40s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</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>14s</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 | 0.0852 0.0000 0.0852 | 32.0000</item>
- <item>2 | 2.50 | 0.0827 0.0011 0.0838 | 29.4886</item>
- <item>3 | 2.50 | 0.0819 0.0017 0.0837 | 26.9772</item>
- <item>4 | 2.50 | 0.0816 0.0020 0.0835 | 24.6107</item>
- <item>5 | 2.50 | 0.0813 0.0021 0.0834 | 22.6548</item>
- <item>6 | 2.50 | 0.0810 0.0022 0.0832 | 20.6989</item>
- <item>7 | 2.50 | 0.0807 0.0023 0.0830 | 18.9688</item>
- <item>8 | 2.50 | 0.0804 0.0024 0.0828 | 17.4455</item>
- <item>9 | 2.50 | 0.0801 0.0025 0.0826 | 15.9223</item>
- <item>10 | 2.50 | 0.0798 0.0026 0.0824 | 14.6627</item>
- <item>11 | 2.50 | 0.0795 0.0027 0.0822 | 13.4764</item>
- <item>12 | 2.50 | 0.0792 0.0028 0.0819 | 12.3015</item>
- <item>13 | 2.50 | 0.0788 0.0029 0.0817 | 11.3776</item>
- <item>14 | 2.50 | 0.0785 0.0029 0.0815 | 10.4537</item>
- <item>15 | 2.25 | 0.0795 0.0030 0.0825 | 9.5920</item>
- <item>16 | 2.25 | 0.0766 0.0045 0.0811 | 8.8725</item>
- <item>17 | 2.25 | 0.0754 0.0050 0.0804 | 8.1530</item>
- <item>18 | 2.25 | 0.0746 0.0053 0.0799 | 7.5234</item>
- <item>29 | 2.00 | 0.0772 0.0025 0.0798 | 3.3283</item>
- <item>30 | 2.00 | 0.0718 0.0049 0.0767 | 3.1221</item>
- <item>31 | 2.00 | 0.0698 0.0059 0.0756 | 2.9160</item>
- <item>43 | 1.75 | 0.0690 0.0034 0.0724 | 1.5785</item>
- <item>44 | 1.75 | 0.0643 0.0059 0.0702 | 1.5194</item>
- <item>45 | 1.75 | 0.0626 0.0068 0.0694 | 1.4626</item>
- <item>57 | 1.50 | 0.0613 0.0050 0.0663 | 1.0900</item>
- <item>58 | 1.50 | 0.0578 0.0073 0.0651 | 1.0730</item>
- <item>59 | 1.50 | 0.0565 0.0081 0.0646 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 184s</item>
- <item>Prepare output 12s</item>
- <item>196s</item>
- <item>Jacobian determinant (RMS): 0.011 0.040 0.062 0.087 0.113 | 0.120731</item>
- <item>Template Matching: 0.085 0.224 0.209 0.188 0.170 | 0.169520</item>
- <item>Write result maps: 43s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 32s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 48s</item>
- <item>104s</item>
- <item>Create initial surface 94s</item>
- <item>Topology correction: 107s</item>
- <item>Surface refinement: 99s</item>
- <item>Reduction of surface collisions with optimization: 84s</item>
- <item>Spherical mapping with areal smoothing 90s</item>
- <item>Spherical registration 311s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 29s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 49s</item>
- <item>102s</item>
- <item>Create initial surface 97s</item>
- <item>Topology correction: 102s</item>
- <item>Surface refinement: 84s</item>
- <item>Reduction of surface collisions with optimization: 83s</item>
- <item>Spherical mapping with areal smoothing 107s</item>
- <item>Spherical registration 351s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5207 0.6065 mm</item>
- <item>Surface intensity / position RMSE: 0.0655 / 0.0707</item>
- <item>Euler number / defect number / defect size: 34.0 / 15.5 / 1.23%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2613068/ds/LMU_1/sub-0025361/ses-1/surf/lh.thickness.sub-0025361_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2613068/ds/LMU_1/sub-0025361/ses-1/surf/rh.thickness.sub-0025361_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2613068/ds/LMU_1/sub-0025361/ses-1/sub-0025361_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 1935s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 20s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 63s</item>
- <item>ROI estimation of 'lpba40' atlas 18s</item>
- <item>ROI estimation of 'hammers' atlas 42s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 13s</item>
- <item>ROI estimation of 'aal3' atlas 21s</item>
- <item>ROI estimation of 'mori' atlas 33s</item>
- <item>ROI estimation of 'anatomy3' atlas 45s</item>
- <item>ROI estimation of 'julichbrain' atlas 58s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 42s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 87s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 111s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
- <item>Write results 10s</item>
- <item>591s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2613068/ds/LMU_1/sub-0025361/ses-1/report/catreport_sub-0025361_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 60 minute(s) and 15 second(s).</item>
- <item>Image Quality Rating (IQR): 74.38% (C)</item>
- <item>GM volume (GMV): 48.52% (781.60 / 1610.72 ml)</item>
- <item>GM thickness (GMT): 2.52 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2613068/ds/LMU_1/sub-0025361/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2613068/ds/LMU_1/sub-0025361/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2613068/ds/LMU_1/sub-0025361/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|