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- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_2529/ds/sub-season105</path>
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- <F>/var/lib/condor/execute/dir_2529/ds/sub-season105/sub-season105_ses-2_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_2529/ds/sub-season105/mri/msub-season105_ses-2_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_2529/ds/sub-season105/mri/p0sub-season105_ses-2_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season105/..son105_ses-2_acq-MPrageHiRes_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>
- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
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- <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>20</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>
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- </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>
- <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/cobra.nii</td>
- <td>0</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/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>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </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>
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- <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>
- <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>
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- </regmethod>
- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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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>
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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>22</SurfaceEulerNumber>
- <SurfaceDefectArea>0.836059835771784</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0732001885771751</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0796716213226318</SurfacePositionRMSE>
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- <res_RMS>0.876671360866484</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[10.2349996566772 301.88720703125 764.256408691406 1099.59191894531]</tissue_mn>
- <tissue_mnr>[0.00930799730122089 0.27454474568367 0.695036351680756 0.999999940395355]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[15.8512496476309 127.757537338524 99.6002695175633 63.1250424795489]</tissue_std>
- <tissue_stdr>[0.0145510155707598 0.117277942597866 0.0914303362369537 0.0579470694065094]</tissue_stdr>
- <contrast>338.486145019531</contrast>
- <contrastr>0.30782887339592</contrastr>
- <NCR>0.112463429570198</NCR>
- <ICR>0.2797871530056</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.76000907987856 1.75000006369637 1.74999997581989]</res_vx_vol>
- <res_RMS>1.75334272173297</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>3.465900182724</contrastr>
- <NCR>1.94549858570099</NCR>
- <ICR>1.15373802185059</ICR>
- <SurfaceEulerNumber>2.02040816326531</SurfaceEulerNumber>
- <SurfaceDefectArea>1.20901495894295</SurfaceDefectArea>
- <SurfaceDefectNumber>1.575</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.46400380134583</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.59343242645264</SurfacePositionRMSE>
- <IQR>1.8664491305652</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>20220712-175537</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>22</SurfaceEulerNumber>
- <SurfaceDefectArea>0.836059835771784</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0732001885771751</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0796716213226318</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>22</EC_abs>
- <defect_size>0.836059835771784</defect_size>
- <vol_abs_CGW>[241.943929112317 714.479371330273 456.606210838687 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.1360144355515</vol_abs_WMH>
- <vol_rel_WMH>0.000803956624034985</vol_rel_WMH>
- <surf_TSA>1981.4292620343</surf_TSA>
- <vol_TIV>1413.02951128128</vol_TIV>
- <vol_rel_CGW>[0.171223549954687 0.505636552970796 0.323139897074517 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.52949352317139 0.594556141772227]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55713200569153 0.728314732536227 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.96958119558321 0.238977672666818 0.292973193530837;2.57105648273032 0.16786867551366 0.414832583213809;3.16772117365539 0.248875767663737 0.292194223255354]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.856654081388656 0.386751341460412 0.635634184068059;4.00137720426851 0.319761451487084 0.364365815931941]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00404365378716</vol_TIV>
- <vol_rel_CGW>[0.924991917289644 6.93097257490653 3.6533745882636 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0803956624035</vol_rel_WMH>
- <surf_TSA>8.62062905664868</surf_TSA>
- <SQR>5.67212104503425</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.2939088003976 1 1 6983.76755692166 0.333776907269038]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00718342419713736 0 0.155347347259521]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[842.992052302928 399.641550305468 337.894399918128 552.73093807611 2275.0217078776 5986.96884953035]</SPMvols0>
- <SPMvols1>[763.02743987545 375.780205897492 221.368765821239 434.76756159424 1456.02720387411 6639.86522324474]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[355.809692382812 799.93310546875 1078.17248535156]</T3th>
- <Tth>
- <T3th>[0 0 16.1184272766113 355.809692382812 799.93310546875 1078.17248535156 1439.35388183594 2970.28247070312]</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>[0.0208557713776827 0.0769708082079887 0.085451640188694 0 0]</dtc>
- <ll>[0.083378462468972 0 0.083378462468972 0;0.19188297267149 0.0108828630481734 0.202765835719664 2320.74877929688;0.19188297267149 0.0108828630481734 0.202765835719664 2320.74877929688]</ll>
- <rmsdtc>[0.0461222045123577 0.103146940469742 0.115026295185089]</rmsdtc>
- <rmsgdt>[0.0331518985331059 0.0474518798291683 0.0583121106028557]</rmsgdt>
- <rmsdt>0.115026295185089</rmsdt>
- <dt>0.085451640188694</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>[0.0102162091061473 0.0384239107370377 0.0544842332601547 0.0634917989373207 0.0707579180598259 0.0800341963768005]</dtc>
- <ll>[0.0841356134552936 0 0.0841356134552936 0;0.220710347985348 0.0146941973824786 0.235404545367827 7521.59228515625;0.20063114221383 0.0175183924481251 0.218149534661955 12608.197265625;0.180041900953563 0.019828064602438 0.199869965556001 21380.046875;0.162685700799095 0.023266566267643 0.185952267066738 40701.4375;0.162685700799095 0.023266566267643 0.185952267066738 40701.4375]</ll>
- <rmsdtc>[0.0120628960430622 0.0446397289633751 0.0666154772043228 0.0935174077749252 0.118668429553509 0.126567736268044]</rmsdtc>
- <rmsgdt>[0.00331786810420454 0.0132638067007065 0.0296763218939304 0.0519511736929417 0.0718339383602142 0.0782901868224144]</rmsgdt>
- <rmsdt>0.126567736268044</rmsdt>
- <dt>0.0800341963768005</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season105_ses-2_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 48s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 10s</item>
- <item>Estimate background 12s</item>
- <item>Initial correction 23s</item>
- <item>Refine background 5s</item>
- <item>Final correction 16s</item>
- <item>Final scaling 11s</item>
- <item>88s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 16s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 145s</item>
- <item>SPM preprocessing 1 (estimate 2): 149s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 28s</item>
- <item>Update Segmentation 33s</item>
- <item>Update Skull-Stripping 73s</item>
- <item>Update probability maps 15s</item>
- <item>149s</item>
- <item>Global intensity correction: 28s</item>
- <item>SANLM denoising after intensity normalization (medium): 13s</item>
- <item>Fast Optimized Shooting registration 50s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 8s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.00) 27s</item>
- <item>Estimate local tissue thresholds (WM) 30s</item>
- <item>Estimate local tissue thresholds (GM) 40s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 34s</item>
- <item>149s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 16s</item>
- <item>Major structures 7s</item>
- <item>Ventricle detection 25s</item>
- <item>Blood vessel detection 16s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 46s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 7s</item>
- <item>Final corrections 8s</item>
- <item>128s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 63s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 8s</item>
- <item>Level 1 cleanup (brain masking) 5s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
- <item>20s</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 | 0.0841 0.0000 0.0841 | 32.0000</item>
- <item>2 | 2.50 | 0.0813 0.0012 0.0825 | 29.4886</item>
- <item>3 | 2.50 | 0.0804 0.0019 0.0823 | 26.9772</item>
- <item>4 | 2.50 | 0.0799 0.0022 0.0821 | 24.6107</item>
- <item>5 | 2.50 | 0.0796 0.0023 0.0819 | 22.6548</item>
- <item>6 | 2.50 | 0.0792 0.0025 0.0817 | 20.6989</item>
- <item>7 | 2.50 | 0.0789 0.0026 0.0815 | 18.9688</item>
- <item>8 | 2.50 | 0.0786 0.0027 0.0813 | 17.4455</item>
- <item>9 | 2.50 | 0.0782 0.0028 0.0810 | 15.9223</item>
- <item>10 | 2.50 | 0.0779 0.0029 0.0808 | 14.6627</item>
- <item>11 | 2.50 | 0.0775 0.0030 0.0805 | 13.4764</item>
- <item>12 | 2.50 | 0.0771 0.0031 0.0802 | 12.3015</item>
- <item>13 | 2.50 | 0.0768 0.0032 0.0800 | 11.3776</item>
- <item>14 | 2.50 | 0.0764 0.0033 0.0797 | 10.4537</item>
- <item>15 | 2.25 | 0.0766 0.0034 0.0800 | 9.5920</item>
- <item>16 | 2.25 | 0.0736 0.0049 0.0785 | 8.8725</item>
- <item>29 | 2.00 | 0.0755 0.0022 0.0777 | 3.3283</item>
- <item>30 | 2.00 | 0.0691 0.0048 0.0739 | 3.1221</item>
- <item>31 | 2.00 | 0.0669 0.0058 0.0727 | 2.9160</item>
- <item>43 | 1.75 | 0.0661 0.0034 0.0695 | 1.5785</item>
- <item>44 | 1.75 | 0.0616 0.0058 0.0674 | 1.5194</item>
- <item>45 | 1.75 | 0.0600 0.0066 0.0666 | 1.4626</item>
- <item>57 | 1.50 | 0.0588 0.0048 0.0636 | 1.0900</item>
- <item>58 | 1.50 | 0.0554 0.0070 0.0624 | 1.0730</item>
- <item>59 | 1.50 | 0.0542 0.0078 0.0620 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 229s</item>
- <item>Prepare output 14s</item>
- <item>244s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.067 0.094 0.119 | 0.126568</item>
- <item>Template Matching: 0.084 0.221 0.201 0.180 0.163 | 0.162686</item>
- <item>Write result maps: 42s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 43s</item>
- <item>CSF distance: 19s</item>
- <item>PBT2x thickness: 57s</item>
- <item>128s</item>
- <item>Create initial surface 100s</item>
- <item>Topology correction: 116s</item>
- <item>Surface refinement: 108s</item>
- <item>Reduction of surface collisions with optimization: 90s</item>
- <item>Spherical mapping with areal smoothing 103s</item>
- <item>Spherical registration 277s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 43s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 58s</item>
- <item>129s</item>
- <item>Create initial surface 103s</item>
- <item>Topology correction: 115s</item>
- <item>Surface refinement: 104s</item>
- <item>Reduction of surface collisions with optimization: 94s</item>
- <item>Spherical mapping with areal smoothing 106s</item>
- <item>Spherical registration 269s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5296 0.5942 mm</item>
- <item>Surface intensity / position RMSE: 0.0732 / 0.0797</item>
- <item>Euler number / defect number / defect size: 22.0 / 11.5 / 0.84%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2529/ds/sub-season105/surf/lh.thickness.sub-season105_ses-2_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2529/ds/sub-season105/surf/rh.thickness.sub-season105_ses-2_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2529/ds/sub-season105/sub-season105_ses-2_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1959s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 18s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 66s</item>
- <item>ROI estimation of 'lpba40' atlas 19s</item>
- <item>ROI estimation of 'hammers' atlas 46s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 16s</item>
- <item>ROI estimation of 'aal3' atlas 27s</item>
- <item>ROI estimation of 'mori' atlas 41s</item>
- <item>ROI estimation of 'anatomy3' atlas 59s</item>
- <item>ROI estimation of 'julichbrain' atlas 82s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 121s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 180s</item>
- <item>Write results 181s</item>
- <item>748s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2529/ds/sub-season105/report/catreport_sub-season105_ses-2_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 70 minute(s) and 13 second(s).</item>
- <item>Image Quality Rating (IQR): 86.34% (B)</item>
- <item>GM volume (GMV): 50.56% (714.48 / 1413.03 ml)</item>
- <item>GM thickness (GMT): 2.53 0.59 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2529/ds/sub-season105/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2529/ds/sub-season105/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2529/ds/sub-season105/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|