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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>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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- <biasreg>0.001</biasreg>
- <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>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.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/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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- <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>
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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>
- <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>
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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>
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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>
- </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/julichbrain.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/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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- <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>
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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_600Parcels_17Networks_order.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>/var/lib/condor/execute/dir_2170455/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
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- <td>[false]</td>
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- </atlas>
- <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>
- </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>
- </tr>
- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </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>
- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
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- <regstr>0.5</regstr>
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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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- </darteltpms>
- <shootingtpms>
- <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>
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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>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.179013682337713</SurfaceDefectArea>
- <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0650465786457062</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0633803755044937</SurfacePositionRMSE>
- <res_vx_vol>[1.0000000362426 1.00000000944653 1.00000000596579]</res_vx_vol>
- <res_vx_voli>[1.0000000339426 1.00000001623443 1.00000000939836]</res_vx_voli>
- <res_RMS>1.00000001721831</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 74.0250015258789 226.800003051758 350.953002929688]</tissue_mn>
- <tissue_mnr>[0 0.210925683379173 0.64624035358429 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[12.8574464100517 38.3943357153929 40.0275254184454 25.1587305784218]</tissue_std>
- <tissue_stdr>[0.0366358086466789 0.109400220215321 0.114053808152676 0.0716868937015533]</tissue_stdr>
- <contrast>124.15299987793</contrast>
- <contrastr>0.353759616613388</contrastr>
- <res_ECR>0.422084927558899</res_ECR>
- <NCR>0.143666312098503</NCR>
- <ICR>0.301231414079666</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.0000000724852 2.00000001889306 2.00000001193159]</res_vx_vol>
- <res_RMS>2.00000003443662</res_RMS>
- <res_ECR>3.05145359039307</res_ECR>
- <res_BB>1</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>2.77693891525269</contrastr>
- <NCR>2.39342975616455</NCR>
- <ICR>1.20692312717438</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.04475342058443</SurfaceDefectArea>
- <SurfaceDefectNumber>1.475</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.30093157291412</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.26760745048523</SurfacePositionRMSE>
- <SIQR>2.71473853690181</SIQR>
- <IQR>2.25408323716587</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>20231031-020317</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.179013682337713</SurfaceDefectArea>
- <SurfaceDefectNumber>9.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0650465786457062</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0633803755044937</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.179013682337713</defect_size>
- <vol_abs_CGW>[321.380972087574 588.298729165774 400.641235633064 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.648643175898073</vol_abs_WMH>
- <vol_rel_WMH>0.000495026186057426</vol_rel_WMH>
- <surf_TSA>1644.19885308139</surf_TSA>
- <vol_TIV>1310.32093688641</vol_TIV>
- <vol_rel_CGW>[0.245268897901639 0.448973005471233 0.305758096627128 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.50874947350968 0.680056634733312]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.50293612480164 0.845262919235055 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.80937123340654 0.296089858198295 0.287515087507544;2.53070790441354 0.201905864082585 0.455182558841279;3.2821272319065 0.315918607908006 0.257302353651177]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.78670347320834 0.21807779869465 0.540036604895905;4.33984712325824 0.330347781898283 0.459963395104095]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.18922087895647</vol_TIV>
- <vol_rel_CGW>[2.25482934449783 5.91330828791726 3.34120144804468 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04950261860574</vol_rel_WMH>
- <surf_TSA>8.40568120011958</surf_TSA>
- <SQR>4.84221825498713</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10813.4405585674 0.395187438128027]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00143560254946351 0.00124959950335324 0.0275807902216911]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[684.409385871997 367.401865025365 471.710733984705 867.82211444594 720.793090000354 8213.71532070786]</SPMvols0>
- <SPMvols1>[607.884977391456 342.64147923653 303.290178852945 658.187415682361 636.513520273483 8266.03162970697]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[77.2166976928711 242.879501342773 341.027404785156]</T3th>
- <Tth>
- <T3th>[-4.31412982940674 -4.3141303062439 4.86639881134033 77.2166976928711 242.879501342773 341.027404785156 472.932739257812 805.399780273438]</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>[0.0227061975747347 0.101468950510025 0.116322219371796 0 0]</dtc>
- <ll>[0.0920165795810512 0 0.0920165795810512 0;0.195670412940567 0.017249715285284 0.212920128225851 3678.46728515625;0.195670412940567 0.017249715285284 0.212920128225851 3678.46728515625]</ll>
- <rmsdtc>[0.0511851124465466 0.134451001882553 0.157773658633232]</rmsdtc>
- <rmsgdt>[0.0365199185907841 0.0623476691544056 0.0812350213527679]</rmsgdt>
- <rmsdt>0.157773658633232</rmsdt>
- <dt>0.116322219371796</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>[0.0108523964881897 0.0495643317699432 0.0668528527021408 0.0792240351438522 0.0870727449655533 0.100272625684738]</dtc>
- <ll>[0.0912164383986511 0 0.0912164383986511 0;0.224041178266178 0.0233581425518926 0.247399320818071 11956.44921875;0.200195573020875 0.0248249880464339 0.225020561067309 17866.841796875;0.174805498983559 0.0252384174922932 0.200043916475852 27213.87890625;0.156133885642292 0.0271920577564963 0.183325943398788 47568.5078125;0.156133885642292 0.0271920577564963 0.183325943398788 47568.5078125]</ll>
- <rmsdtc>[0.0129789812490344 0.050428356975317 0.08539929240942 0.119008667767048 0.14691361784935 0.154533475637436]</rmsdtc>
- <rmsgdt>[0.00379243213683367 0.0163295995444059 0.0368949584662914 0.0596861802041531 0.0776863545179367 0.0832037851214409]</rmsgdt>
- <rmsdt>0.154533475637436</rmsdt>
- <dt>0.100272625684738</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026175/ses-2/sub-0026175_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 66s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>41s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 14s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 94s</item>
- <item>SPM preprocessing 1 (estimate 2): 72s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 20s</item>
- <item>Update Segmentation 22s</item>
- <item>Update Skull-Stripping 47s</item>
- <item>Update probability maps 10s</item>
- <item>98s</item>
- <item>Global intensity correction: 19s</item>
- <item>SANLM denoising after intensity normalization (medium): 30s</item>
- <item>Fast Optimized Shooting registration 44s</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) 17s</item>
- <item>Estimate local tissue thresholds (WM) 21s</item>
- <item>Estimate local tissue thresholds (GM) 33s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 49s</item>
- <item>130s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 16s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.25) 25s</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>74s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 35s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>13s</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 | 0.0912 0.0000 0.0912 | 32.0000</item>
- <item>2 | 2.50 | 0.0877 0.0015 0.0892 | 29.4886</item>
- <item>3 | 2.50 | 0.0866 0.0023 0.0889 | 26.9772</item>
- <item>4 | 2.50 | 0.0861 0.0026 0.0887 | 24.6107</item>
- <item>5 | 2.50 | 0.0856 0.0028 0.0884 | 22.6548</item>
- <item>6 | 2.50 | 0.0852 0.0030 0.0882 | 20.6989</item>
- <item>7 | 2.50 | 0.0848 0.0031 0.0879 | 18.9688</item>
- <item>8 | 2.50 | 0.0844 0.0033 0.0876 | 17.4455</item>
- <item>9 | 2.50 | 0.0840 0.0034 0.0873 | 15.9223</item>
- <item>10 | 2.50 | 0.0835 0.0036 0.0870 | 14.6627</item>
- <item>11 | 2.50 | 0.0830 0.0037 0.0867 | 13.4764</item>
- <item>12 | 2.50 | 0.0825 0.0038 0.0864 | 12.3015</item>
- <item>13 | 2.50 | 0.0820 0.0040 0.0860 | 11.3776</item>
- <item>14 | 2.50 | 0.0816 0.0041 0.0857 | 10.4537</item>
- <item>15 | 2.25 | 0.0827 0.0043 0.0870 | 9.5920</item>
- <item>16 | 2.25 | 0.0787 0.0063 0.0850 | 8.8725</item>
- <item>17 | 2.25 | 0.0769 0.0071 0.0840 | 8.1530</item>
- <item>18 | 2.25 | 0.0756 0.0075 0.0832 | 7.5234</item>
- <item>19 | 2.25 | 0.0747 0.0078 0.0825 | 6.9630</item>
- <item>29 | 2.00 | 0.0760 0.0040 0.0800 | 3.3283</item>
- <item>30 | 2.00 | 0.0692 0.0071 0.0763 | 3.1221</item>
- <item>31 | 2.00 | 0.0667 0.0083 0.0750 | 2.9160</item>
- <item>43 | 1.75 | 0.0650 0.0048 0.0699 | 1.5785</item>
- <item>44 | 1.75 | 0.0600 0.0075 0.0675 | 1.5194</item>
- <item>45 | 1.75 | 0.0583 0.0084 0.0667 | 1.4626</item>
- <item>57 | 1.50 | 0.0564 0.0063 0.0627 | 1.0900</item>
- <item>58 | 1.50 | 0.0531 0.0084 0.0615 | 1.0730</item>
- <item>59 | 1.50 | 0.0520 0.0091 0.0611 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 213s</item>
- <item>Prepare output 13s</item>
- <item>226s</item>
- <item>Jacobian determinant (RMS): 0.013 0.050 0.085 0.119 0.147 | 0.154533</item>
- <item>Template Matching: 0.091 0.224 0.200 0.175 0.156 | 0.156134</item>
- <item>Write result maps: 37s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 33s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 49s</item>
- <item>105s</item>
- <item>Create initial surface 93s</item>
- <item>Topology correction: 82s</item>
- <item>Surface refinement: 75s</item>
- <item>Reduction of surface collisions with optimization: 58s</item>
- <item>Spherical mapping with areal smoothing 86s</item>
- <item>Spherical registration 338s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 30s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 48s</item>
- <item>101s</item>
- <item>Create initial surface 88s</item>
- <item>Topology correction: 80s</item>
- <item>Surface refinement: 72s</item>
- <item>Reduction of surface collisions with optimization: 56s</item>
- <item>Spherical mapping with areal smoothing 89s</item>
- <item>Spherical registration 357s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5088 0.6800 mm</item>
- <item>Surface intensity / position RMSE: 0.0650 / 0.0634</item>
- <item>Euler number / defect number / defect size: 8.0 / 9.5 / 0.18%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2170455/ds/UM/sub-0026175/ses-2/surf/lh.thickness.sub-0026175_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2170455/ds/UM/sub-0026175/ses-2/surf/rh.thickness.sub-0026175_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2170455/ds/UM/sub-0026175/ses-2/sub-0026175_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 1782s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 36s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 25s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 14s</item>
- <item>ROI estimation of 'mori' atlas 22s</item>
- <item>ROI estimation of 'anatomy3' atlas 31s</item>
- <item>ROI estimation of 'julichbrain' atlas 41s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>412s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2170455/ds/UM/sub-0026175/ses-2/report/catreport_sub-0026175_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 54 minute(s) and 59 second(s).</item>
- <item>Image Quality Rating (IQR): 82.46% (B-)</item>
- <item>GM volume (GMV): 44.90% (588.30 / 1310.32 ml)</item>
- <item>GM thickness (GMT): 2.51 0.68 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2170455/ds/UM/sub-0026175/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2170455/ds/UM/sub-0026175/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2170455/ds/UM/sub-0026175/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|