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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>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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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>
- <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>
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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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- <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>
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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/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>
- <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>
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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>
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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_3274552/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>
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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>
- </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>
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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>
- <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>
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- <shooting>
- <shootingtpm>
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- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- <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>
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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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- </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>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.740661252266404</SurfaceDefectArea>
- <SurfaceDefectNumber>19</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0796287953853607</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0747319236397743</SurfacePositionRMSE>
- <res_vx_vol>[1.20000001373999 0.499999985854638 0.5]</res_vx_vol>
- <res_vx_voli>[0.800000049407821 0.799999989816249 0.800000011920929]</res_vx_voli>
- <res_RMS>0.804155876023759</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[21.17799949646 58.1269989013672 199.427001953125 345.282989501953]</tissue_mn>
- <tissue_mnr>[0.0613351948559284 0.168345972895622 0.577575504779816 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[19.7404634355222 35.3362174806568 35.4836886006458 26.6416378160199]</tissue_std>
- <tissue_stdr>[0.0609076209366322 0.109027072787285 0.10948208719492 0.0822006464004517]</tissue_stdr>
- <contrast>118.545295715332</contrast>
- <contrastr>0.343327939510345</contrastr>
- <res_ECR>0.313576102256775</res_ECR>
- <NCR>0.157757937908173</NCR>
- <ICR>0</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.40000002747998 0.999999971709276 1]</res_vx_vol>
- <res_RMS>1.60831175204752</res_RMS>
- <res_ECR>2.49783706665039</res_ECR>
- <res_BB>NaN</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>2.93341422080994</contrastr>
- <NCR>2.59572124481201</NCR>
- <ICR>0.5</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.1851653130666</SurfaceDefectArea>
- <SurfaceDefectNumber>1.95</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.59257590770721</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.49463844299316</SurfacePositionRMSE>
- <SIQR>2.42780721252429</SIQR>
- <IQR>2.38668931634854</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>20231031-012716</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.740661252266404</SurfaceDefectArea>
- <SurfaceDefectNumber>19</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0796287953853607</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0747319236397743</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>0.740661252266404</defect_size>
- <vol_abs_CGW>[224.71421019371 880.355390305745 516.716908328473 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.904750238233965</vol_abs_WMH>
- <vol_rel_WMH>0.000557872588845145</vol_rel_WMH>
- <surf_TSA>2199.74166345384</surf_TSA>
- <vol_TIV>1621.78650882793</vol_TIV>
- <vol_rel_CGW>[0.138559674143616 0.542830628762587 0.318609697093797 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.71770812697191 0.613899716235378]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.73906636238098 0.760331361349977 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.09838363523028 0.259548526127276 0.286750449225257;2.75019572889522 0.181443068918338 0.427613289421223;3.39274441063578 0.26966523546038 0.28563626135352]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.962442906729871 0.44218285559847 0.589333588663347;4.24593075979948 0.271607921673776 0.410666411336653]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.08630443737685</vol_TIV>
- <vol_rel_CGW>[0.5 7.59896962576486 3.57201323803515 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05578725888451</vol_rel_WMH>
- <surf_TSA>8.62390344016434</surf_TSA>
- <SQR>6.21602442212158</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11796.4798013387 0.49238734223558]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00134717067703605 0.00104477594140917 0.121636882424355]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1017.69510029389 460.554084722227 564.821475858759 352.378888473119 1119.88865838803 8906.94471801245]</SPMvols0>
- <SPMvols1>[871.541769538358 435.093744647457 286.593002165384 317.52438585267 786.1365941332 9099.72703421177]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[80.1829986572266 209.147903442383 346.3583984375]</T3th>
- <Tth>
- <T3th>[-188.045074462891 -30.9889678955078 8.41627216339111 80.1829986572266 209.147903442383 346.3583984375 479.446105957031 1078.97265625]</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>[0.0192730519920588 0.0643172562122345 0.0707956179976463 0 0]</dtc>
- <ll>[0.0829522788119154 0 0.0829522788119154 0;0.204410823167158 0.0088301603676749 0.213240983534832 1883.01403808594;0.204410823167158 0.0088301603676749 0.213240983534832 1883.01403808594]</ll>
- <rmsdtc>[0.040447823703289 0.0874822363257408 0.0985576882958412]</rmsdtc>
- <rmsgdt>[0.0285508818924427 0.0424489416182041 0.0529597364366055]</rmsgdt>
- <rmsdt>0.0985576882958412</rmsdt>
- <dt>0.0707956179976463</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>[0.0079492349177599 0.0277415663003922 0.039749838411808 0.0500803254544735 0.0586948394775391 0.0658338740468025]</dtc>
- <ll>[0.0814179056369952 0 0.0814179056369952 0;0.219516941391941 0.0105093540140415 0.230026295405983 5379.4755859375;0.203864054302276 0.0143431016069622 0.218207155909239 10322.90234375;0.185151754960715 0.0179202269058735 0.203071981866588 19322.87890625;0.168030194591943 0.0219713909942705 0.190001585586214 38435.71875;0.168030194591943 0.0219713909942705 0.190001585586214 38435.71875]</ll>
- <rmsdtc>[0.00953814759850502 0.0336479470133781 0.0528570897877216 0.0814372822642326 0.110658414661884 0.118010267615318]</rmsdtc>
- <rmsgdt>[0.00291039398871362 0.0116546237841249 0.0280030090361834 0.0515368431806564 0.0742885023355484 0.0810285806655884]</rmsgdt>
- <rmsdt>0.118010267615318</rmsdt>
- <dt>0.0658338740468025</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026036/ses-1/sub-0026036_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 232s</item>
- <item>Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 10s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 5s</item>
- <item>Final correction 8s</item>
- <item>Final scaling 7s</item>
- <item>55s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 27s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 107s</item>
- <item>SPM preprocessing 1 (estimate 2): 39s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 26s</item>
- <item>Update Segmentation 29s</item>
- <item>Update Skull-Stripping 67s</item>
- <item>Update probability maps 14s</item>
- <item>135s</item>
- <item>Global intensity correction: 23s</item>
- <item>SANLM denoising after intensity normalization (medium): 48s</item>
- <item>Fast Optimized Shooting registration 36s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.00) 22s</item>
- <item>Estimate local tissue thresholds (WM) 30s</item>
- <item>Estimate local tissue thresholds (GM) 45s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 63s</item>
- <item>176s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 16s</item>
- <item>Major structures 7s</item>
- <item>Ventricle detection 43s</item>
- <item>Blood vessel detection 18s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 56s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 10s</item>
- <item>159s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 49s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 7s</item>
- <item>Level 1 cleanup (brain masking) 6s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
- <item>22s</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 | 0.0814 0.0000 0.0814 | 32.0000</item>
- <item>2 | 2.50 | 0.0796 0.0009 0.0805 | 29.4886</item>
- <item>3 | 2.50 | 0.0791 0.0014 0.0805 | 26.9772</item>
- <item>4 | 2.50 | 0.0788 0.0016 0.0804 | 24.6107</item>
- <item>5 | 2.50 | 0.0786 0.0017 0.0803 | 22.6548</item>
- <item>6 | 2.50 | 0.0784 0.0017 0.0801 | 20.6989</item>
- <item>7 | 2.50 | 0.0782 0.0018 0.0800 | 18.9688</item>
- <item>8 | 2.50 | 0.0780 0.0019 0.0798 | 17.4455</item>
- <item>9 | 2.50 | 0.0778 0.0019 0.0797 | 15.9223</item>
- <item>10 | 2.50 | 0.0775 0.0020 0.0795 | 14.6627</item>
- <item>11 | 2.50 | 0.0773 0.0020 0.0794 | 13.4764</item>
- <item>12 | 2.50 | 0.0771 0.0021 0.0792 | 12.3015</item>
- <item>13 | 2.50 | 0.0768 0.0022 0.0790 | 11.3776</item>
- <item>14 | 2.50 | 0.0766 0.0022 0.0788 | 10.4537</item>
- <item>15 | 2.25 | 0.0757 0.0023 0.0780 | 9.5920</item>
- <item>16 | 2.25 | 0.0732 0.0035 0.0767 | 8.8725</item>
- <item>29 | 2.00 | 0.0752 0.0016 0.0768 | 3.3283</item>
- <item>30 | 2.00 | 0.0697 0.0039 0.0736 | 3.1221</item>
- <item>31 | 2.00 | 0.0680 0.0048 0.0727 | 2.9160</item>
- <item>43 | 1.75 | 0.0677 0.0027 0.0704 | 1.5785</item>
- <item>44 | 1.75 | 0.0632 0.0052 0.0683 | 1.5194</item>
- <item>45 | 1.75 | 0.0617 0.0060 0.0677 | 1.4626</item>
- <item>57 | 1.50 | 0.0606 0.0043 0.0649 | 1.0900</item>
- <item>58 | 1.50 | 0.0571 0.0066 0.0637 | 1.0730</item>
- <item>59 | 1.50 | 0.0560 0.0073 0.0633 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 180s</item>
- <item>Prepare output 12s</item>
- <item>193s</item>
- <item>Jacobian determinant (RMS): 0.010 0.034 0.053 0.081 0.111 | 0.118010</item>
- <item>Template Matching: 0.081 0.220 0.204 0.185 0.168 | 0.168030</item>
- <item>Write result maps: 233s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 24s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 39s</item>
- <item>83s</item>
- <item>Create initial surface 71s</item>
- <item>Topology correction: 84s</item>
- <item>Surface refinement: 71s</item>
- <item>Reduction of surface collisions with optimization: 70s</item>
- <item>Spherical mapping with areal smoothing 79s</item>
- <item>Spherical registration 224s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 29s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 40s</item>
- <item>88s</item>
- <item>Create initial surface 67s</item>
- <item>Topology correction: 81s</item>
- <item>Surface refinement: 75s</item>
- <item>Reduction of surface collisions with optimization: 66s</item>
- <item>Spherical mapping with areal smoothing 76s</item>
- <item>Spherical registration 219s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.7177 0.6136 mm</item>
- <item>Surface intensity / position RMSE: 0.0796 / 0.0747</item>
- <item>Euler number / defect number / defect size: 30.0 / 19.0 / 0.74%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/surf/lh.thickness.sub-0026036_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/surf/rh.thickness.sub-0026036_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/sub-0026036_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1483s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 15s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 52s</item>
- <item>ROI estimation of 'lpba40' atlas 15s</item>
- <item>ROI estimation of 'hammers' atlas 36s</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 31s</item>
- <item>ROI estimation of 'anatomy3' atlas 42s</item>
- <item>ROI estimation of 'julichbrain' atlas 56s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 99s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 152s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 12s</item>
- <item>Write results 13s</item>
- <item>615s</item>
- <item>Quality check: 41s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/report/catreport_sub-0026036_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 62 minute(s) and 50 second(s).</item>
- <item>Image Quality Rating (IQR): 81.13% (B-)</item>
- <item>GM volume (GMV): 54.28% (880.36 / 1621.79 ml)</item>
- <item>GM thickness (GMT): 2.72 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|