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- <fnames>../Utah_1/sub-0026032/ses-1/sub-0026032_ses-1_run-1_T1w</fnames>
- </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>
- <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>
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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>
- <td>
- <item>csf</item>
- <item>gm</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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- <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>
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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>
- <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_1682866/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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- <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>
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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>
- </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>
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- <shooting>
- <shootingtpm>
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- </shootingtpm>
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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_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>
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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>
- <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>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.440832462014265</SurfaceDefectArea>
- <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0743789225816727</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0703832730650902</SurfacePositionRMSE>
- <res_vx_vol>[1.19999994057992 0.500000008644889 0.500000004965203]</res_vx_vol>
- <res_vx_voli>[0.799999961621475 0.500000007356011 0.500000004774325]</res_vx_voli>
- <res_RMS>0.804155845385271</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[22.80299949646 64.2109985351562 238.826995849609 382.605010986328]</tissue_mn>
- <tissue_mnr>[0.0595993213355541 0.167825818061829 0.624212920665741 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[13.690348730008 40.8798715933978 40.8731412132275 25.6287484775948]</tissue_std>
- <tissue_stdr>[0.0380496717989445 0.113617688417435 0.113598980009556 0.0712301433086395]</tissue_stdr>
- <contrast>135.217468261719</contrast>
- <contrastr>0.353412687778473</contrastr>
- <res_ECR>0.348524153232574</res_ECR>
- <NCR>0.199772030115128</NCR>
- <ICR>0.240579947829247</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.39999988115984 1.00000001728978 1.00000000993041]</res_vx_vol>
- <res_RMS>1.60831169077054</res_RMS>
- <res_ECR>2.67614364624023</res_ECR>
- <res_BB>1</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>2.78214311599731</contrastr>
- <NCR>3.19885206222534</NCR>
- <ICR>1.05649793148041</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.11020811550357</SurfaceDefectArea>
- <SurfaceDefectNumber>1.925</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.48757839202881</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.40766549110413</SurfacePositionRMSE>
- <SIQR>2.86555026851647</SIQR>
- <IQR>2.93485482096388</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>20231031-035334</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.440832462014265</SurfaceDefectArea>
- <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0743789225816727</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0703832730650902</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.440832462014265</defect_size>
- <vol_abs_CGW>[240.00454254419 781.603032446641 587.678416652919 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.905299586376233</vol_abs_WMH>
- <vol_rel_WMH>0.000562547360181484</vol_rel_WMH>
- <surf_TSA>2324.81438577823</surf_TSA>
- <vol_TIV>1609.28599164375</vol_TIV>
- <vol_rel_CGW>[0.149137284354936 0.485683114440274 0.36517960120479 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.43923634145063 0.587513787998215]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.44136762619019 0.694274640704644 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.8831104998254 0.233272285890856 0.313099973481835;2.47708878270829 0.16761398202938 0.419496154866083;3.0863432664011 0.247655380248029 0.267403871652082]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.858236948236486 0.396355741330261 0.549753941112687;3.96751901435605 0.360143528501237 0.450246058887313]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.97528096917175</vol_TIV>
- <vol_rel_CGW>[0.528327664420553 6.57261340589573 4.40839801014349 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05625473601815</vol_rel_WMH>
- <surf_TSA>8.6239906743541</surf_TSA>
- <SQR>5.40189332089164</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11796.4797369792 0.3911991030314]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00105163105763495 0.000848515424877405 0.0747416764497757]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[960.828320745783 511.56757924201 516.492569713461 982.550955524803 1026.19006350962 8420.48969366259]</SPMvols0>
- <SPMvols1>[812.760808962714 482.947378352038 262.466489462541 815.685354775719 948.856212010064 8476.94038722596]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[84.8142013549805 243.15510559082 380.872314453125]</T3th>
- <Tth>
- <T3th>[-98.9309997558594 -59.3293151855469 8.47610473632812 84.8142013549805 243.15510559082 380.872314453125 528.9013671875 1043.54382324219]</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>[0.024166377261281 0.0905937850475311 0.101553022861481 0 0]</dtc>
- <ll>[0.0874578346963786 0 0.0874578346963786 0;0.194168658674407 0.0128575298680263 0.207026188542434 2741.84252929688;0.194168658674407 0.0128575298680263 0.207026188542434 2741.84252929688]</ll>
- <rmsdtc>[0.0528567545115948 0.11935868114233 0.1319550126791]</rmsdtc>
- <rmsgdt>[0.0375320166349411 0.050969522446394 0.0620500035583973]</rmsgdt>
- <rmsdt>0.1319550126791</rmsdt>
- <dt>0.101553022861481</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>[0.0113662015646696 0.0448300838470459 0.0608212240040302 0.0698889791965485 0.076440341770649 0.0864635035395622]</dtc>
- <ll>[0.086911800378794 0 0.086911800378794 0;0.221168437118437 0.0180804181929182 0.239248855311355 9254.9140625;0.200659777800009 0.0191347060199948 0.219794483820004 13771.4775390625;0.179576833929658 0.0207526939660169 0.200329527895675 22377.048828125;0.161550745475613 0.0238019472413515 0.185352692716965 41638.0078125;0.161550745475613 0.0238019472413515 0.185352692716965 41638.0078125]</ll>
- <rmsdtc>[0.0132356584072113 0.0488266274333 0.0743010714650154 0.100990310311317 0.124440044164658 0.130948260426521]</rmsdtc>
- <rmsgdt>[0.00364072015509009 0.014281184412539 0.0306699685752392 0.0521275885403156 0.0710168480873108 0.0761445090174675]</rmsgdt>
- <rmsdt>0.130948260426521</rmsdt>
- <dt>0.0864635035395622</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026032/ses-1/sub-0026032_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 327s</item>
- <item>Internal resampling (1.20x0.50x0.50mm > 0.80x0.50x0.50mm): 5s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 11s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 24s</item>
- <item>Refine background 5s</item>
- <item>Final correction 14s</item>
- <item>Final scaling 30s</item>
- <item>132s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 42s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 86s</item>
- <item>SPM preprocessing 1 (estimate 2): 74s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 102s</item>
- <item>Update Segmentation 118s</item>
- <item>Update Skull-Stripping 379s</item>
- <item>Update probability maps 105s</item>
- <item>704s</item>
- <item>Global intensity correction: 91s</item>
- <item>SANLM denoising after intensity normalization (medium): 307s</item>
- <item>Fast Optimized Shooting registration 105s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 21s</item>
- <item>Prepare partitions 17s</item>
- <item>Prepare segments (LASmod = 1.00) 110s</item>
- <item>Estimate local tissue thresholds (WM) 70s</item>
- <item>Estimate local tissue thresholds (GM) 85s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 346s</item>
- <item>671s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 28s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 23s</item>
- <item>Blood vessel detection 16s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 41s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 26s</item>
- <item>148s</item>
- <item>Blood vessel correction (BVCstr=0.50): 10s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 159s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 28s</item>
- <item>Level 1 cleanup (brain masking) 15s</item>
- <item>Level 2 cleanup (CSF correction) 8s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 19s</item>
- <item>71s</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 | 0.0826 0.0021 0.0847 | 26.9772</item>
- <item>4 | 2.50 | 0.0821 0.0024 0.0845 | 24.6107</item>
- <item>5 | 2.50 | 0.0817 0.0026 0.0843 | 22.6548</item>
- <item>6 | 2.50 | 0.0814 0.0027 0.0841 | 20.6989</item>
- <item>7 | 2.50 | 0.0810 0.0028 0.0839 | 18.9688</item>
- <item>8 | 2.50 | 0.0806 0.0030 0.0836 | 17.4455</item>
- <item>9 | 2.50 | 0.0803 0.0031 0.0833 | 15.9223</item>
- <item>10 | 2.50 | 0.0799 0.0032 0.0831 | 14.6627</item>
- <item>11 | 2.50 | 0.0795 0.0033 0.0828 | 13.4764</item>
- <item>12 | 2.50 | 0.0791 0.0034 0.0825 | 12.3015</item>
- <item>13 | 2.50 | 0.0787 0.0035 0.0822 | 11.3776</item>
- <item>14 | 2.50 | 0.0783 0.0036 0.0819 | 10.4537</item>
- <item>15 | 2.25 | 0.0786 0.0037 0.0823 | 9.5920</item>
- <item>16 | 2.25 | 0.0751 0.0054 0.0805 | 8.8725</item>
- <item>17 | 2.25 | 0.0737 0.0060 0.0797 | 8.1530</item>
- <item>29 | 2.00 | 0.0752 0.0028 0.0779 | 3.3283</item>
- <item>30 | 2.00 | 0.0691 0.0053 0.0744 | 3.1221</item>
- <item>31 | 2.00 | 0.0669 0.0064 0.0733 | 2.9160</item>
- <item>43 | 1.75 | 0.0660 0.0037 0.0697 | 1.5785</item>
- <item>44 | 1.75 | 0.0614 0.0061 0.0675 | 1.5194</item>
- <item>45 | 1.75 | 0.0599 0.0069 0.0668 | 1.4626</item>
- <item>57 | 1.50 | 0.0583 0.0051 0.0634 | 1.0900</item>
- <item>58 | 1.50 | 0.0550 0.0072 0.0622 | 1.0730</item>
- <item>59 | 1.50 | 0.0539 0.0079 0.0618 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 214s</item>
- <item>Prepare output 43s</item>
- <item>257s</item>
- <item>Jacobian determinant (RMS): 0.013 0.049 0.074 0.101 0.124 | 0.130948</item>
- <item>Template Matching: 0.087 0.221 0.201 0.180 0.162 | 0.161551</item>
- <item>Write result maps: 363s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 54s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 65s</item>
- <item>150s</item>
- <item>Create initial surface 119s</item>
- <item>Topology correction: 130s</item>
- <item>Surface refinement: 121s</item>
- <item>Reduction of surface collisions with optimization: 105s</item>
- <item>Spherical mapping with areal smoothing 125s</item>
- <item>Spherical registration 343s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 46s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 65s</item>
- <item>141s</item>
- <item>Create initial surface 117s</item>
- <item>Topology correction: 131s</item>
- <item>Surface refinement: 121s</item>
- <item>Reduction of surface collisions with optimization: 102s</item>
- <item>Spherical mapping with areal smoothing 116s</item>
- <item>Spherical registration 342s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4392 0.5875 mm</item>
- <item>Surface intensity / position RMSE: 0.0744 / 0.0704</item>
- <item>Euler number / defect number / defect size: 18.0 / 18.5 / 0.44%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/surf/lh.thickness.sub-0026032_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/surf/rh.thickness.sub-0026032_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/sub-0026032_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2433s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 51s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 183s</item>
- <item>ROI estimation of 'lpba40' atlas 52s</item>
- <item>ROI estimation of 'hammers' atlas 125s</item>
- <item>ROI estimation of 'thalamus' atlas 10s</item>
- <item>ROI estimation of 'ibsr' atlas 44s</item>
- <item>ROI estimation of 'aal3' atlas 70s</item>
- <item>ROI estimation of 'mori' atlas 106s</item>
- <item>ROI estimation of 'anatomy3' atlas 151s</item>
- <item>ROI estimation of 'julichbrain' atlas 198s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 79s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 136s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 310s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 476s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 39s</item>
- <item>Write results 40s</item>
- <item>2031s</item>
- <item>Quality check: 57s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/report/catreport_sub-0026032_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 138 minute(s) and 47 second(s).</item>
- <item>Image Quality Rating (IQR): 75.65% (C)</item>
- <item>GM volume (GMV): 48.57% (781.60 / 1609.29 ml)</item>
- <item>GM thickness (GMT): 2.44 0.59 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1682866/ds/Utah_1/sub-0026032/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|