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- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_17538/ds/sub-f3300jh</path>
- <file>sub-f3300jh_ses-wave1bas_T1w</file>
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- <F>/var/lib/condor/execute/dir_17538/ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_17538/ds/sub-f3300jh/mri/msub-f3300jh_ses-wave1bas_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_17538/ds/sub-f3300jh/mri/p0sub-f3300jh_ses-wave1bas_T1w.nii</Fp0>
- <fnames>../ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_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>
- <accstr>0.5</accstr>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
- <redspmres>0</redspmres>
- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
- </opts>
- <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_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>24</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>
- </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/lpba40.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/cobra.nii</td>
- <td>0</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/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <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/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </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/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </tr>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </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>
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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>
- </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>
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- <regmethod>
- <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>
- </shooting>
- </regmethod>
- <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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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_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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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </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>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.217665075130327</SurfaceDefectArea>
- <SurfaceDefectNumber>6</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.064399391412735</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0582683086395264</SurfacePositionRMSE>
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- <res_RMS>0.800000555468531</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[19.7399997711182 261.143218994141 735.237426757812 938.3759765625]</tissue_mn>
- <tissue_mnr>[0.0210363436490297 0.278292745351791 0.783521175384521 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[12.7761632976498 118.034846266423 106.198314785908 69.426036946276]</tissue_std>
- <tissue_stdr>[0.0139077538624406 0.12848924100399 0.115604348480701 0.0755751356482506]</tissue_stdr>
- <contrast>207.503662109375</contrast>
- <contrastr>0.22113062441349</contrastr>
- <NCR>0.112345807254314</NCR>
- <ICR>1.07797241210938</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.6000032846804 1.6000000477366 1.60000000039197]</res_vx_vol>
- <res_RMS>1.60000111093706</res_RMS>
- <res_BB>0.5</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>4.76637411117554</contrastr>
- <NCR>1.9438099861145</NCR>
- <ICR>3.13336420059204</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.05441626878258</SurfaceDefectArea>
- <SurfaceDefectNumber>1.3</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.2879878282547</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.16536617279053</SurfacePositionRMSE>
- <IQR>1.82560194883737</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>1980</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>20220711-110946</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.217665075130327</SurfaceDefectArea>
- <SurfaceDefectNumber>6</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.064399391412735</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0582683086395264</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.217665075130327</defect_size>
- <vol_abs_CGW>[274.214402571987 699.103409128744 481.999811637313 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.694986225875034</vol_abs_WMH>
- <vol_rel_WMH>0.000477549515466563</vol_rel_WMH>
- <surf_TSA>2052.89385644481</surf_TSA>
- <vol_TIV>1455.31762333804</vol_TIV>
- <vol_rel_CGW>[0.188422374727398 0.480378577100729 0.331199048171873 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.50415535931855 0.564509870625738]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.48765802383423 0.657735626666136 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.99918223663765 0.216903621967928 0.319757307384143;2.53223206946088 0.157723013213434 0.428479684891039;3.13423189968374 0.236133402000751 0.251763007724818]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.984295841963057 0.419203125764767 0.538249911253106;3.962892113203 0.305554868293012 0.461750088746894]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.07255796478297</vol_TIV>
- <vol_rel_CGW>[1.2338788564547 6.47734513471137 3.7981150892937 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04775495154666</vol_rel_WMH>
- <surf_TSA>8.62286574409196</surf_TSA>
- <SQR>5.30614746810225</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.126508213141026 1 1 8930.26320975013 0.466266271979959]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0246964748948812 0.0211831126362085 0.305531054735184]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[814.12001839769 449.057538821186 412.764682866944 1014.62286892202 1904.97199075405 6259.46221512536]</SPMvols0>
- <SPMvols1>[726.465585162623 423.135330636877 267.205712395136 1182.84830109164 1643.44155915036 5980.56213143027]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[348.591400146484 753.481201171875 1010.08538818359]</T3th>
- <Tth>
- <T3th>[0 0 26.4899120330811 348.591400146484 753.481201171875 1010.08538818359 1340.83239746094 2944.3564453125]</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>[0.0255445633083582 0.0884926021099091 0.0985573902726173 0 0]</dtc>
- <ll>[0.0906119650008441 0 0.0906119650008441 0;0.197154563729789 0.0123243721164003 0.209478935846189 2628.14770507812;0.197154563729789 0.0123243721164003 0.209478935846189 2628.14770507812]</ll>
- <rmsdtc>[0.0518485009670258 0.115621738135815 0.126282587647438]</rmsdtc>
- <rmsgdt>[0.0362673029303551 0.04841398447752 0.0587462969124317]</rmsgdt>
- <rmsdt>0.126282587647438</rmsdt>
- <dt>0.0985573902726173</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>[0.0129414163529873 0.051770094782114 0.0678045600652695 0.0767102688550949 0.0836074650287628 0.0949295610189438]</dtc>
- <ll>[0.0911099223802719 0 0.0911099223802719 0;0.218863812576313 0.022672951007326 0.241536763583639 11605.716796875;0.197244283998322 0.0212761211255335 0.218520405123855 15312.6796875;0.176169211595034 0.0217059480498659 0.197875159644899 23404.916015625;0.158320890637853 0.024342350161031 0.182663240798884 42583.36328125;0.158320890637853 0.024342350161031 0.182663240798884 42583.36328125]</ll>
- <rmsdtc>[0.0151377860456705 0.0562881380319595 0.0823897868394852 0.107612811028957 0.130772918462753 0.13760831952095]</rmsdtc>
- <rmsgdt>[0.00389859825372696 0.0149646261706948 0.0306335035711527 0.0506707765161991 0.0691475868225098 0.0747102126479149]</rmsgdt>
- <rmsdt>0.13760831952095</rmsdt>
- <dt>0.0949295610189438</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 183s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 16s</item>
- <item>Estimate background 16s</item>
- <item>Initial correction 15s</item>
- <item>Refine background 8s</item>
- <item>Final correction 13s</item>
- <item>Final scaling 15s</item>
- <item>98s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 19s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 175s</item>
- <item>SPM preprocessing 1 (estimate 2): 88s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 40s</item>
- <item>Update Segmentation 47s</item>
- <item>Update Skull-Stripping 101s</item>
- <item>Update probability maps 20s</item>
- <item>208s</item>
- <item>Global intensity correction: 40s</item>
- <item>SANLM denoising after intensity normalization (medium): 37s</item>
- <item>Fast Optimized Shooting registration 62s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 12s</item>
- <item>Prepare partitions 6s</item>
- <item>Prepare segments (LASmod = 1.00) 38s</item>
- <item>Estimate local tissue thresholds (WM) 40s</item>
- <item>Estimate local tissue thresholds (GM) 57s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 62s</item>
- <item>222s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 21s</item>
- <item>Major structures 9s</item>
- <item>Ventricle detection 37s</item>
- <item>Blood vessel detection 25s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 65s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 5s</item>
- <item>Side alignment 11s</item>
- <item>Final corrections 11s</item>
- <item>183s</item>
- <item>Blood vessel correction (BVCstr=0.50): 4s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 88s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 11s</item>
- <item>Level 1 cleanup (brain masking) 6s</item>
- <item>Level 2 cleanup (CSF correction) 4s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
- <item>29s</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 | 0.0911 0.0000 0.0911 | 32.0000</item>
- <item>2 | 2.50 | 0.0860 0.0018 0.0878 | 29.4886</item>
- <item>3 | 2.50 | 0.0844 0.0029 0.0873 | 26.9772</item>
- <item>4 | 2.50 | 0.0837 0.0033 0.0869 | 24.6107</item>
- <item>5 | 2.50 | 0.0831 0.0035 0.0866 | 22.6548</item>
- <item>6 | 2.50 | 0.0826 0.0037 0.0863 | 20.6989</item>
- <item>7 | 2.50 | 0.0821 0.0038 0.0859 | 18.9688</item>
- <item>8 | 2.50 | 0.0815 0.0040 0.0855 | 17.4455</item>
- <item>9 | 2.50 | 0.0810 0.0041 0.0851 | 15.9223</item>
- <item>10 | 2.50 | 0.0805 0.0043 0.0848 | 14.6627</item>
- <item>11 | 2.50 | 0.0800 0.0044 0.0844 | 13.4764</item>
- <item>12 | 2.50 | 0.0794 0.0045 0.0839 | 12.3015</item>
- <item>13 | 2.50 | 0.0789 0.0046 0.0835 | 11.3776</item>
- <item>14 | 2.50 | 0.0784 0.0047 0.0831 | 10.4537</item>
- <item>15 | 2.25 | 0.0787 0.0049 0.0835 | 9.5920</item>
- <item>16 | 2.25 | 0.0746 0.0069 0.0815 | 8.8725</item>
- <item>17 | 2.25 | 0.0730 0.0076 0.0805 | 8.1530</item>
- <item>29 | 2.00 | 0.0742 0.0035 0.0776 | 3.3283</item>
- <item>30 | 2.00 | 0.0679 0.0061 0.0740 | 3.1221</item>
- <item>31 | 2.00 | 0.0657 0.0071 0.0728 | 2.9160</item>
- <item>43 | 1.75 | 0.0648 0.0041 0.0689 | 1.5785</item>
- <item>44 | 1.75 | 0.0603 0.0064 0.0667 | 1.5194</item>
- <item>45 | 1.75 | 0.0587 0.0072 0.0660 | 1.4626</item>
- <item>57 | 1.50 | 0.0571 0.0054 0.0625 | 1.0900</item>
- <item>58 | 1.50 | 0.0539 0.0074 0.0613 | 1.0730</item>
- <item>59 | 1.50 | 0.0528 0.0081 0.0609 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 267s</item>
- <item>Prepare output 19s</item>
- <item>286s</item>
- <item>Jacobian determinant (RMS): 0.015 0.056 0.082 0.108 0.131 | 0.137608</item>
- <item>Template Matching: 0.091 0.219 0.197 0.176 0.158 | 0.158321</item>
- <item>Write result maps: 59s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 56s</item>
- <item>CSF distance: 24s</item>
- <item>PBT2x thickness: 66s</item>
- <item>155s</item>
- <item>Create initial surface 116s</item>
- <item>Topology correction: 133s</item>
- <item>Surface refinement: 112s</item>
- <item>Reduction of surface collisions with optimization: 110s</item>
- <item>Spherical mapping with areal smoothing 120s</item>
- <item>Spherical registration 302s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 103s</item>
- <item>CSF distance: 23s</item>
- <item>PBT2x thickness: 64s</item>
- <item>199s</item>
- <item>Create initial surface 111s</item>
- <item>Topology correction: 131s</item>
- <item>Surface refinement: 138s</item>
- <item>Reduction of surface collisions with optimization: 101s</item>
- <item>Spherical mapping with areal smoothing 116s</item>
- <item>Spherical registration 289s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5040 0.5645 mm</item>
- <item>Surface intensity / position RMSE: 0.0644 / 0.0583</item>
- <item>Euler number / defect number / defect size: 8.0 / 6.0 / 0.22%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/surf/lh.thickness.sub-f3300jh_ses-wave1bas_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/surf/rh.thickness.sub-f3300jh_ses-wave1bas_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/sub-f3300jh_ses-wave1bas_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 2286s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 27s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 101s</item>
- <item>ROI estimation of 'lpba40' atlas 29s</item>
- <item>ROI estimation of 'hammers' atlas 72s</item>
- <item>ROI estimation of 'thalamus' atlas 5s</item>
- <item>ROI estimation of 'ibsr' atlas 26s</item>
- <item>ROI estimation of 'aal3' atlas 43s</item>
- <item>ROI estimation of 'mori' atlas 62s</item>
- <item>ROI estimation of 'anatomy3' atlas 91s</item>
- <item>ROI estimation of 'julichbrain' atlas 120s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 45s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 59s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 201s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 284s</item>
- <item>Write results 286s</item>
- <item>1168s</item>
- <item>Quality check: 11s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_17538/ds/sub-f3300jh/report/catreport_sub-f3300jh_ses-wave1bas_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 90 minute(s) and 51 second(s).</item>
- <item>Image Quality Rating (IQR): 86.74% (B+)</item>
- <item>GM volume (GMV): 48.04% (699.10 / 1455.32 ml)</item>
- <item>GM thickness (GMT): 2.50 0.56 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_17538/ds/sub-f3300jh/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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