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- <S>
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- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
- <tol>0.0001</tol>
- <accstr>0.5</accstr>
- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
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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>
- <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>
- <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/lpba40.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/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>
- </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>
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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>
- <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_200Parcels_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_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>
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- <td>[false]</td>
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- <tr>
- <td>/var/lib/condor/execute/dir_110026/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
- </td>
- <td>[false]</td>
- </tr>
- </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>
- </tr>
- <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>
- </tr>
- <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>
- </tr>
- <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>
- <NB>0</NB>
- <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>
- <lazy>0</lazy>
- <affmod>0</affmod>
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- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <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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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
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- </darteltpms>
- <shootingtpms>
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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>
- </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>32</SurfaceEulerNumber>
- <SurfaceDefectArea>1.01654489062999</SurfaceDefectArea>
- <SurfaceDefectNumber>19.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0726307556033134</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0707269608974457</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>198.022277832031</res_BB>
- <tissue_mn>[14.7629995346069 99.129997253418 272.265014648438 433.994995117188]</tissue_mn>
- <tissue_mnr>[0.0340165197849274 0.228412762284279 0.627345979213715 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.90422549072034 46.0049149520446 47.1574653352337 31.2513491548222]</tissue_std>
- <tissue_stdr>[0.0188540611416101 0.109736174345016 0.112485371530056 0.0745442882180214]</tissue_stdr>
- <contrast>154.579467773438</contrast>
- <contrastr>0.356177985668182</contrastr>
- <res_ECR>0.365952908992767</res_ECR>
- <NCR>0.16277340054512</NCR>
- <ICR>0.258203119039536</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.76506567001343</res_ECR>
- <res_BB>10.5</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.74066352844238</contrastr>
- <NCR>2.66772031784058</NCR>
- <ICR>1.10020613670349</ICR>
- <SurfaceEulerNumber>2.53061224489796</SurfaceEulerNumber>
- <SurfaceDefectArea>1.2541362226575</SurfaceDefectArea>
- <SurfaceDefectNumber>1.975</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.4526150226593</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.41453921794891</SurfacePositionRMSE>
- <SIQR>2.59861666512704</SIQR>
- <IQR>2.47557229987702</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>20231031-004109</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>32</SurfaceEulerNumber>
- <SurfaceDefectArea>1.01654489062999</SurfaceDefectArea>
- <SurfaceDefectNumber>19.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0726307556033134</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0707269608974457</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>32</EC_abs>
- <defect_size>1.01654489062999</defect_size>
- <vol_abs_CGW>[221.575529411765 828.062607843137 531.359419607843 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.844329411764706</vol_abs_WMH>
- <vol_rel_WMH>0.000534048524047154</vol_rel_WMH>
- <surf_TSA>2256.15663852684</surf_TSA>
- <vol_TIV>1580.99755686275</vol_TIV>
- <vol_rel_CGW>[0.14014919153414 0.523759574610795 0.336091233855065 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.61033086451338 0.613691222049025]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.59490537643433 0.694502339709066 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.02468928511653 0.238775478152594 0.318509814394445;2.63134412571761 0.176770463860968 0.410217652557084;3.28267183123226 0.252074313558884 0.271272533048471]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[1.03348282832482 0.371792972155899 0.512919186366135;4.14608935097347 0.310484490295887 0.487080813633865]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.74188646149991</vol_TIV>
- <vol_rel_CGW>[0.5 7.25645787734905 3.88597761952344 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05340485240472</vol_rel_WMH>
- <surf_TSA>8.62396542613412</surf_TSA>
- <SQR>5.93908292161906</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.648 0.36322741263419]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00162176508456469 0.000908792135305703 0.289919376373291]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[973.136094117647 472.919278431373 412.60168627451 572.100250980392 1876.72950588235 5841.60072156863]</SPMvols0>
- <SPMvols1>[855.930576470588 445.149337254902 228.751843137255 452.902439215686 1049.43679215686 6339.52787843137]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[116.608901977539 286.258392333984 425.714599609375]</T3th>
- <Tth>
- <T3th>[-6.62904977798462 -6.62904691696167 8.85637855529785 116.608901977539 286.258392333984 425.714599609375 580.267456054688 1010.87573242188]</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>[0.0219134483486414 0.0745075643062592 0.0822066888213158 0 0]</dtc>
- <ll>[0.0865018675927402 0 0.0865018675927402 0;0.200398512676555 0.0112218112647891 0.211620323941344 2393.02880859375;0.200398512676555 0.0112218112647891 0.211620323941344 2393.02880859375]</ll>
- <rmsdtc>[0.0474849827587605 0.0982009395956993 0.10925605148077]</rmsdtc>
- <rmsgdt>[0.0341408029198647 0.0467039868235588 0.0574063956737518]</rmsgdt>
- <rmsdt>0.10925605148077</rmsdt>
- <dt>0.0822066888213158</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>[0.00988567899912596 0.0376403518021107 0.0513686500489712 0.0617744475603104 0.0694995522499084 0.0781956985592842]</dtc>
- <ll>[0.0868990376996524 0 0.0868990376996524 0;0.223649450549451 0.0178065972222222 0.241456047771673 9114.751953125;0.20630072775638 0.0191527905107355 0.225453518267116 13784.4931640625;0.185987046867581 0.0212558409427306 0.207242887810311 22919.578125;0.168737456076618 0.0247872869819585 0.193524743058577 43361.71484375;0.168737456076618 0.0247872869819585 0.193524743058577 43361.71484375]</ll>
- <rmsdtc>[0.0116791110485792 0.0419783666729927 0.064991183578968 0.0927325412631035 0.119113363325596 0.125213831663132]</rmsdtc>
- <rmsgdt>[0.00347665697336197 0.0137293394654989 0.0302017126232386 0.0522145703434944 0.0737237483263016 0.0789221227169037]</rmsgdt>
- <rmsdt>0.125213831663132</rmsdt>
- <dt>0.0781956985592842</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025322/ses-1/sub-0025322_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 62s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>42s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 93s</item>
- <item>SPM preprocessing 1 (estimate 2): 130s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 19s</item>
- <item>Update Segmentation 22s</item>
- <item>Update Skull-Stripping 44s</item>
- <item>Update probability maps 8s</item>
- <item>93s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 34s</item>
- <item>Fast Optimized Shooting registration 39s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 5s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 18s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 36s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 45s</item>
- <item>131s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 19s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 33s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 4s</item>
- <item>88s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 40s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 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 | 0.0869 0.0000 0.0869 | 32.0000</item>
- <item>2 | 2.50 | 0.0836 0.0014 0.0850 | 29.4886</item>
- <item>3 | 2.50 | 0.0827 0.0021 0.0848 | 26.9772</item>
- <item>4 | 2.50 | 0.0822 0.0024 0.0846 | 24.6107</item>
- <item>5 | 2.50 | 0.0818 0.0025 0.0844 | 22.6548</item>
- <item>6 | 2.50 | 0.0815 0.0026 0.0841 | 20.6989</item>
- <item>7 | 2.50 | 0.0812 0.0028 0.0839 | 18.9688</item>
- <item>8 | 2.50 | 0.0808 0.0029 0.0837 | 17.4455</item>
- <item>9 | 2.50 | 0.0804 0.0030 0.0834 | 15.9223</item>
- <item>10 | 2.50 | 0.0800 0.0031 0.0831 | 14.6627</item>
- <item>11 | 2.50 | 0.0797 0.0032 0.0828 | 13.4764</item>
- <item>12 | 2.50 | 0.0793 0.0032 0.0825 | 12.3015</item>
- <item>13 | 2.50 | 0.0789 0.0034 0.0822 | 11.3776</item>
- <item>14 | 2.50 | 0.0785 0.0034 0.0819 | 10.4537</item>
- <item>15 | 2.25 | 0.0797 0.0035 0.0833 | 9.5920</item>
- <item>16 | 2.25 | 0.0760 0.0053 0.0813 | 8.8725</item>
- <item>17 | 2.25 | 0.0745 0.0059 0.0805 | 8.1530</item>
- <item>29 | 2.00 | 0.0772 0.0027 0.0799 | 3.3283</item>
- <item>30 | 2.00 | 0.0709 0.0054 0.0763 | 3.1221</item>
- <item>31 | 2.00 | 0.0688 0.0064 0.0752 | 2.9160</item>
- <item>43 | 1.75 | 0.0683 0.0037 0.0720 | 1.5785</item>
- <item>44 | 1.75 | 0.0636 0.0062 0.0698 | 1.5194</item>
- <item>45 | 1.75 | 0.0620 0.0071 0.0691 | 1.4626</item>
- <item>57 | 1.50 | 0.0610 0.0052 0.0662 | 1.0900</item>
- <item>58 | 1.50 | 0.0575 0.0075 0.0650 | 1.0730</item>
- <item>59 | 1.50 | 0.0562 0.0083 0.0645 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 214s</item>
- <item>Prepare output 14s</item>
- <item>228s</item>
- <item>Jacobian determinant (RMS): 0.012 0.042 0.065 0.093 0.119 | 0.125214</item>
- <item>Template Matching: 0.087 0.224 0.206 0.186 0.169 | 0.168737</item>
- <item>Write result maps: 35s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 41s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 66s</item>
- <item>136s</item>
- <item>Create initial surface 114s</item>
- <item>Topology correction: 131s</item>
- <item>Surface refinement: 114s</item>
- <item>Reduction of surface collisions with optimization: 105s</item>
- <item>Spherical mapping with areal smoothing 123s</item>
- <item>Spherical registration 341s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 39s</item>
- <item>CSF distance: 23s</item>
- <item>PBT2x thickness: 69s</item>
- <item>139s</item>
- <item>Create initial surface 121s</item>
- <item>Topology correction: 131s</item>
- <item>Surface refinement: 134s</item>
- <item>Reduction of surface collisions with optimization: 109s</item>
- <item>Spherical mapping with areal smoothing 131s</item>
- <item>Spherical registration 366s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6103 0.6137 mm</item>
- <item>Surface intensity / position RMSE: 0.0726 / 0.0707</item>
- <item>Euler number / defect number / defect size: 32.0 / 19.5 / 1.02%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-1/surf/lh.thickness.sub-0025322_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-1/surf/rh.thickness.sub-0025322_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-1/sub-0025322_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 2320s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 8s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 31s</item>
- <item>ROI estimation of 'lpba40' atlas 9s</item>
- <item>ROI estimation of 'hammers' atlas 21s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 13s</item>
- <item>ROI estimation of 'mori' atlas 19s</item>
- <item>ROI estimation of 'anatomy3' atlas 26s</item>
- <item>ROI estimation of 'julichbrain' atlas 35s</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 56s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 9s</item>
- <item>363s</item>
- <item>Quality check: 14s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-1/report/catreport_sub-0025322_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 64 minute(s) and 17 second(s).</item>
- <item>Image Quality Rating (IQR): 80.24% (B-)</item>
- <item>GM volume (GMV): 52.38% (828.06 / 1581.00 ml)</item>
- <item>GM thickness (GMT): 2.61 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_110026/ds/UPSM_1/sub-0025322/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|