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- <filedata>
- <path>/var/lib/condor/execute/dir_12430/ds/sub-season202</path>
- <file>sub-season202_ses-3_acq-MPrageHiRes_T1w</file>
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- <F>/var/lib/condor/execute/dir_12430/ds/sub-season202/sub-season202_ses-3_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_12430/ds/sub-season202/mri/msub-season202_ses-3_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_12430/ds/sub-season202/mri/p0sub-season202_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season202/..son202_ses-3_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>
- <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>32</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>
- </td>
- <td>[false]</td>
- </tr>
- <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>
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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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- <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>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_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>34</SurfaceEulerNumber>
- <SurfaceDefectArea>1.37068747083974</SurfaceDefectArea>
- <SurfaceDefectNumber>20.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0719823613762856</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0728897899389267</SurfacePositionRMSE>
- <res_vx_vol>[0.880000750521057 0.87500001466776 0.874999988192853]</res_vx_vol>
- <res_vx_voli>[0.880000749198923 0.875000015357782 0.874999986826101]</res_vx_voli>
- <res_RMS>0.876670087304549</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.66300010681152 405.941497802734 969.421691894531 1403.39831542969]</tissue_mn>
- <tissue_mnr>[0.00688542984426022 0.28925609588623 0.690767347812653 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[21.3167315883543 160.517529127038 129.971667328751 80.968178950981]</tissue_std>
- <tissue_stdr>[0.0152946775779128 0.115170747041702 0.0932542011141777 0.0580943748354912]</tissue_stdr>
- <contrast>436.985412597656</contrast>
- <contrastr>0.311376631259918</contrastr>
- <NCR>0.106331631541252</NCR>
- <ICR>0.314212620258331</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.76000150104211 1.75000002933552 1.74999997638571]</res_vx_vol>
- <res_RMS>1.7533401746091</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>3.41268372535706</contrastr>
- <NCR>1.85747385025024</NCR>
- <ICR>1.2391185760498</ICR>
- <SurfaceEulerNumber>2.63265306122449</SurfaceEulerNumber>
- <SurfaceDefectArea>1.34267186770993</SurfaceDefectArea>
- <SurfaceDefectNumber>2.025</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.43964719772339</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.45779585838318</SurfacePositionRMSE>
- <IQR>1.81062046202351</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>20220712-172012</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>34</SurfaceEulerNumber>
- <SurfaceDefectArea>1.37068747083974</SurfaceDefectArea>
- <SurfaceDefectNumber>20.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0719823613762856</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0728897899389267</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>34</EC_abs>
- <defect_size>1.37068747083974</defect_size>
- <vol_abs_CGW>[264.260104630682 860.839038019208 624.899431124118 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.16707867298953</vol_abs_WMH>
- <vol_rel_WMH>0.000666902642367663</vol_rel_WMH>
- <surf_TSA>2400.26101628311</surf_TSA>
- <vol_TIV>1749.99857377401</vol_TIV>
- <vol_rel_CGW>[0.15100589714241 0.491908422623878 0.357085680233712 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.56025851310359 0.613982882844531]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.56228685379028 0.729706257535593 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.9682053298438 0.239305602728734 0.305562294054622;2.59341544763761 0.176005812441932 0.424121131259223;3.23846984383387 0.261528603972237 0.270316574686154]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.896503647796489 0.392397699196511 0.539859224095597;4.14493275379973 0.327907366080873 0.460140775904403]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>3.42486749236895</vol_TIV>
- <vol_rel_CGW>[0.561887520517421 6.68441850976792 4.26303305017443 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.06669026423677</vol_rel_WMH>
- <surf_TSA>8.62399795289258</surf_TSA>
- <SQR>5.48476631550123</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.206460748400007 1 1 7848.65993574975 0.312484471584245]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00642769550904632 0.00313432794064283 0.275816470384598]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1037.84177962492 541.900182303602 448.995254363283 781.18151807166 2831.71934778201 4952.60323726375]</SPMvols0>
- <SPMvols1>[914.484445957098 512.088835716606 269.773498063825 1127.64542309856 2525.48330350593 4541.32043154761]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[468.667907714844 1012.30010986328 1384.30383300781]</T3th>
- <Tth>
- <T3th>[0 0 22.5963611602783 468.667907714844 1012.30010986328 1384.30383300781 1842.12182617188 4137.2373046875]</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>[0.0209838971495628 0.0739423036575317 0.0813489332795143 0 0]</dtc>
- <ll>[0.0829434679145096 0 0.0829434679145096 0;0.191076967896534 0.00994530273657314 0.201022270633107 2120.81591796875;0.191076967896534 0.00994530273657314 0.201022270633107 2120.81591796875]</ll>
- <rmsdtc>[0.0466193296015263 0.0967613160610199 0.106882832944393]</rmsdtc>
- <rmsgdt>[0.033439002931118 0.0437671393156052 0.0537460632622242]</rmsgdt>
- <rmsdt>0.106882832944393</rmsdt>
- <dt>0.0813489332795143</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>[0.00972827710211277 0.0356416031718254 0.0493325740098953 0.056864146143198 0.0633099302649498 0.0707598924636841]</dtc>
- <ll>[0.0838246611070059 0 0.0838246611070059 0;0.216663598901099 0.0137929286858974 0.230456527586996 7060.25537109375;0.19704919728308 0.0159947591775425 0.213043956460622 11511.6201171875;0.178606922696685 0.0179753063524324 0.196582229049117 19382.26953125;0.161934030038534 0.0213445431682456 0.18327857320678 37339.140625;0.161934030038534 0.0213445431682456 0.18327857320678 37339.140625]</ll>
- <rmsdtc>[0.0114339357241988 0.0411816835403442 0.0606186985969543 0.0833460465073586 0.106075130403042 0.112727612257004]</rmsdtc>
- <rmsgdt>[0.00334212998859584 0.0127380797639489 0.0276356060057878 0.0470862686634064 0.0659611150622368 0.0715434998273849]</rmsgdt>
- <rmsdt>0.112727612257004</rmsdt>
- <dt>0.0707598924636841</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season202_ses-3_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 46s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 9s</item>
- <item>Initial correction 23s</item>
- <item>Refine background 4s</item>
- <item>Final correction 17s</item>
- <item>Final scaling 10s</item>
- <item>77s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 12s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 114s</item>
- <item>SPM preprocessing 1 (estimate 2): 101s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 22s</item>
- <item>Update Segmentation 29s</item>
- <item>Update Skull-Stripping 56s</item>
- <item>Update probability maps 11s</item>
- <item>117s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 16s</item>
- <item>Fast Optimized Shooting registration 35s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 7s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 23s</item>
- <item>Estimate local tissue thresholds (WM) 26s</item>
- <item>Estimate local tissue thresholds (GM) 38s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 34s</item>
- <item>135s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 6s</item>
- <item>Ventricle detection 42s</item>
- <item>Blood vessel detection 17s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 50s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 5s</item>
- <item>140s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 51s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 7s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>17s</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 | 0.0838 0.0000 0.0838 | 32.0000</item>
- <item>2 | 2.50 | 0.0808 0.0013 0.0821 | 29.4886</item>
- <item>3 | 2.50 | 0.0800 0.0019 0.0819 | 26.9772</item>
- <item>4 | 2.50 | 0.0795 0.0022 0.0817 | 24.6107</item>
- <item>5 | 2.50 | 0.0792 0.0023 0.0815 | 22.6548</item>
- <item>6 | 2.50 | 0.0789 0.0024 0.0813 | 20.6989</item>
- <item>7 | 2.50 | 0.0786 0.0025 0.0811 | 18.9688</item>
- <item>8 | 2.50 | 0.0783 0.0026 0.0809 | 17.4455</item>
- <item>9 | 2.50 | 0.0780 0.0027 0.0806 | 15.9223</item>
- <item>10 | 2.50 | 0.0776 0.0028 0.0804 | 14.6627</item>
- <item>11 | 2.50 | 0.0773 0.0029 0.0801 | 13.4764</item>
- <item>12 | 2.50 | 0.0769 0.0029 0.0799 | 12.3015</item>
- <item>13 | 2.50 | 0.0766 0.0030 0.0796 | 11.3776</item>
- <item>14 | 2.50 | 0.0762 0.0031 0.0793 | 10.4537</item>
- <item>15 | 2.25 | 0.0751 0.0032 0.0783 | 9.5920</item>
- <item>16 | 2.25 | 0.0722 0.0046 0.0768 | 8.8725</item>
- <item>29 | 2.00 | 0.0734 0.0021 0.0754 | 3.3283</item>
- <item>30 | 2.00 | 0.0675 0.0044 0.0720 | 3.1221</item>
- <item>31 | 2.00 | 0.0657 0.0053 0.0710 | 2.9160</item>
- <item>43 | 1.75 | 0.0650 0.0031 0.0680 | 1.5785</item>
- <item>44 | 1.75 | 0.0609 0.0052 0.0661 | 1.5194</item>
- <item>45 | 1.75 | 0.0595 0.0060 0.0655 | 1.4626</item>
- <item>57 | 1.50 | 0.0583 0.0043 0.0626 | 1.0900</item>
- <item>58 | 1.50 | 0.0551 0.0064 0.0615 | 1.0730</item>
- <item>59 | 1.50 | 0.0540 0.0071 0.0611 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 154s</item>
- <item>Prepare output 12s</item>
- <item>167s</item>
- <item>Jacobian determinant (RMS): 0.011 0.041 0.061 0.083 0.106 | 0.112728</item>
- <item>Template Matching: 0.084 0.217 0.197 0.179 0.162 | 0.161934</item>
- <item>Write result maps: 28s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 39s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 53s</item>
- <item>117s</item>
- <item>Create initial surface 98s</item>
- <item>Topology correction: 113s</item>
- <item>Surface refinement: 108s</item>
- <item>Reduction of surface collisions with optimization: 97s</item>
- <item>Spherical mapping with areal smoothing 111s</item>
- <item>Spherical registration 267s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 50s</item>
- <item>111s</item>
- <item>Create initial surface 95s</item>
- <item>Topology correction: 115s</item>
- <item>Surface refinement: 105s</item>
- <item>Reduction of surface collisions with optimization: 96s</item>
- <item>Spherical mapping with areal smoothing 143s</item>
- <item>Spherical registration 274s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5603 0.6139 mm</item>
- <item>Surface intensity / position RMSE: 0.0720 / 0.0729</item>
- <item>Euler number / defect number / defect size: 34.0 / 20.5 / 1.37%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_12430/ds/sub-season202/surf/lh.thickness.sub-season202_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_12430/ds/sub-season202/surf/rh.thickness.sub-season202_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_12430/ds/sub-season202/sub-season202_ses-3_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1957s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 36s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 25s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 13s</item>
- <item>ROI estimation of 'mori' atlas 20s</item>
- <item>ROI estimation of 'anatomy3' atlas 27s</item>
- <item>ROI estimation of 'julichbrain' atlas 37s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 26s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 58s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 87s</item>
- <item>Write results 87s</item>
- <item>377s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_12430/ds/sub-season202/report/catreport_sub-season202_ses-3_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 58 minute(s) and 56 second(s).</item>
- <item>Image Quality Rating (IQR): 86.89% (B+)</item>
- <item>GM volume (GMV): 49.19% (860.84 / 1750.00 ml)</item>
- <item>GM thickness (GMT): 2.56 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_12430/ds/sub-season202/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_12430/ds/sub-season202/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_12430/ds/sub-season202/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|