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- <filedata>
- <path>/var/lib/condor/execute/dir_57358/ds/sub-season214</path>
- <file>sub-season214_ses-3_acq-MPrageHiRes_T1w</file>
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- <F>/var/lib/condor/execute/dir_57358/ds/sub-season214/sub-season214_ses-3_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_57358/ds/sub-season214/mri/msub-season214_ses-3_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_57358/ds/sub-season214/mri/p0sub-season214_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season214/..son214_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>
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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>64</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>
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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>
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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>
- </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/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>
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- </td>
- <td>[false]</td>
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- </atlas>
- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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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>
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- <new_release>0</new_release>
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- <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>
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- <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>52</SurfaceEulerNumber>
- <SurfaceDefectArea>2.98340257802564</SurfaceDefectArea>
- <SurfaceDefectNumber>27</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0785906985402107</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0973872989416122</SurfacePositionRMSE>
- <res_vx_vol>[0.880001910765747 0.875000025500278 0.875000001053985]</res_vx_vol>
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- <res_RMS>0.876670483405125</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[10.3070001602173 316.273040771484 812.005065917969 1176.57397460938]</tissue_mn>
- <tissue_mnr>[0.00876018032431602 0.268808454275131 0.690143644809723 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[35.1193310166956 155.968592802103 110.060892366007 62.0135810756232]</tissue_std>
- <tissue_stdr>[0.0301125999540091 0.133733183145523 0.0943702384829521 0.0531727150082588]</tissue_stdr>
- <contrast>367.790832519531</contrast>
- <contrastr>0.31259474158287</contrastr>
- <NCR>0.0935315936803818</NCR>
- <ICR>0.269517242908478</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.76000382153149 1.75000005100056 1.75000000210797]</res_vx_vol>
- <res_RMS>1.75334096681025</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>3.39441204071045</contrastr>
- <NCR>1.67372369766235</NCR>
- <ICR>1.12826693058014</ICR>
- <SurfaceEulerNumber>3.55102040816327</SurfaceEulerNumber>
- <SurfaceDefectArea>1.74585064450641</SurfaceDefectArea>
- <SurfaceDefectNumber>2.35</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.57181394100189</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.94774603843689</SurfacePositionRMSE>
- <IQR>1.71675235022411</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>20220712-174814</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>52</SurfaceEulerNumber>
- <SurfaceDefectArea>2.98340257802564</SurfaceDefectArea>
- <SurfaceDefectNumber>27</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0785906985402107</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0973872989416122</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>52</EC_abs>
- <defect_size>2.98340257802564</defect_size>
- <vol_abs_CGW>[172.74757532359 737.752791583678 512.886911647826 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.677601110289226</vol_abs_WMH>
- <vol_rel_WMH>0.000476048311305038</vol_rel_WMH>
- <surf_TSA>1997.77816935686</surf_TSA>
- <vol_TIV>1423.38727855509</vol_TIV>
- <vol_rel_CGW>[0.121363720138731 0.518307844041281 0.360328435819988 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.60032176457789 0.667676461586899]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.64896941184998 0.890609451682132 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.91761459050238 0.317773675051187 0.265777455772052;2.62808714047197 0.193142543618913 0.419682995920161;3.30521021126867 0.282574140802445 0.314539548307787]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.716238222637938 0.308471229431119 0.710702188043578;4.17466589559483 0.284033403843584 0.289297811956422]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.01302030557118</vol_TIV>
- <vol_rel_CGW>[0.5 7.15854604959198 4.32127219504288 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0476048311305</vol_rel_WMH>
- <surf_TSA>8.62135585120999</surf_TSA>
- <SQR>5.86681510460534</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.30295991897583 1 1 6894.22471254159 0.333460500401008]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00630701053887606 0 0.181353613734245]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[870.430643743956 450.397719613296 248.202509521768 635.494905904619 2248.64960991677 5998.32281529293]</SPMvols0>
- <SPMvols1>[787.840773855813 427.185076152545 156.7848571141 567.060493826574 1338.57860236887 6613.55999847952]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[369.219909667969 850.114074707031 1162.5009765625]</T3th>
- <Tth>
- <T3th>[0 0 14.8978309631348 369.219909667969 850.114074707031 1162.5009765625 1559.14147949219 2972.72290039062]</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>[0.0190048944205046 0.0658977404236794 0.0717149674892426 0 0]</dtc>
- <ll>[0.0806229046794499 0 0.0806229046794499 0;0.18581955487273 0.00919555501491368 0.195015109887644 1960.93371582031;0.18581955487273 0.00919555501491368 0.195015109887644 1960.93371582031]</ll>
- <rmsdtc>[0.0467615313827991 0.0858950465917587 0.0944933742284775]</rmsdtc>
- <rmsgdt>[0.0342672988772392 0.0387771315872669 0.0474207997322083]</rmsgdt>
- <rmsdt>0.0944933742284775</rmsdt>
- <dt>0.0717149674892426</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>[0.00871637091040611 0.0322940312325954 0.0445018708705902 0.05174919962883 0.0577210448682308 0.0641828924417496]</dtc>
- <ll>[0.0822043243805545 0 0.0822043243805545 0;0.208262820512821 0.0142725818452381 0.222535402358059 7305.77783203125;0.188546295254213 0.0158831883990575 0.20442948365327 11431.3212890625;0.169936901936617 0.0175591656285473 0.187496067565164 18933.556640625;0.153628334304168 0.0203935420159625 0.174021876320131 35675.50390625;0.153628334304168 0.0203935420159625 0.174021876320131 35675.50390625]</ll>
- <rmsdtc>[0.0104958200827241 0.0382802374660969 0.0555646792054176 0.0764089971780777 0.0978711619973183 0.104534387588501]</rmsdtc>
- <rmsgdt>[0.00322354538366199 0.0121928630396724 0.0259412564337254 0.0452000945806503 0.0635979995131493 0.0690911263227463]</rmsgdt>
- <rmsdt>0.104534387588501</rmsdt>
- <dt>0.0641828924417496</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season214_ses-3_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 34s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 9s</item>
- <item>Estimate background 11s</item>
- <item>Initial correction 11s</item>
- <item>Refine background 5s</item>
- <item>Final correction 10s</item>
- <item>Final scaling 9s</item>
- <item>64s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 15s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 123s</item>
- <item>SPM preprocessing 1 (estimate 2): 93s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 25s</item>
- <item>Update Segmentation 30s</item>
- <item>Update Skull-Stripping 66s</item>
- <item>Update probability maps 13s</item>
- <item>135s</item>
- <item>Global intensity correction: 24s</item>
- <item>SANLM denoising after intensity normalization (medium): 14s</item>
- <item>Fast Optimized Shooting registration 43s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 7s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.00) 24s</item>
- <item>Estimate local tissue thresholds (WM) 31s</item>
- <item>Estimate local tissue thresholds (GM) 46s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 39s</item>
- <item>156s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 6s</item>
- <item>Ventricle detection 22s</item>
- <item>Blood vessel detection 17s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 46s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 7s</item>
- <item>117s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 53s</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) 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 | 0.0822 0.0000 0.0822 | 32.0000</item>
- <item>2 | 2.50 | 0.0789 0.0013 0.0803 | 29.4886</item>
- <item>3 | 2.50 | 0.0780 0.0020 0.0800 | 26.9772</item>
- <item>4 | 2.50 | 0.0775 0.0023 0.0798 | 24.6107</item>
- <item>5 | 2.50 | 0.0771 0.0025 0.0796 | 22.6548</item>
- <item>6 | 2.50 | 0.0768 0.0026 0.0794 | 20.6989</item>
- <item>7 | 2.50 | 0.0765 0.0027 0.0792 | 18.9688</item>
- <item>8 | 2.50 | 0.0762 0.0028 0.0789 | 17.4455</item>
- <item>9 | 2.50 | 0.0758 0.0028 0.0787 | 15.9223</item>
- <item>10 | 2.50 | 0.0755 0.0029 0.0784 | 14.6627</item>
- <item>11 | 2.50 | 0.0751 0.0030 0.0781 | 13.4764</item>
- <item>12 | 2.50 | 0.0748 0.0031 0.0778 | 12.3015</item>
- <item>13 | 2.50 | 0.0744 0.0032 0.0775 | 11.3776</item>
- <item>14 | 2.50 | 0.0740 0.0032 0.0772 | 10.4537</item>
- <item>15 | 2.25 | 0.0723 0.0033 0.0756 | 9.5920</item>
- <item>16 | 2.25 | 0.0694 0.0048 0.0742 | 8.8725</item>
- <item>29 | 2.00 | 0.0705 0.0021 0.0726 | 3.3283</item>
- <item>30 | 2.00 | 0.0648 0.0044 0.0692 | 3.1221</item>
- <item>31 | 2.00 | 0.0628 0.0053 0.0681 | 2.9160</item>
- <item>43 | 1.75 | 0.0620 0.0031 0.0650 | 1.5785</item>
- <item>44 | 1.75 | 0.0580 0.0051 0.0631 | 1.5194</item>
- <item>45 | 1.75 | 0.0566 0.0059 0.0625 | 1.4626</item>
- <item>57 | 1.50 | 0.0551 0.0043 0.0594 | 1.0900</item>
- <item>58 | 1.50 | 0.0522 0.0062 0.0584 | 1.0730</item>
- <item>59 | 1.50 | 0.0512 0.0068 0.0580 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 183s</item>
- <item>Prepare output 15s</item>
- <item>199s</item>
- <item>Jacobian determinant (RMS): 0.010 0.038 0.056 0.076 0.098 | 0.104534</item>
- <item>Template Matching: 0.082 0.208 0.189 0.170 0.154 | 0.153628</item>
- <item>Write result maps: 35s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 35s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 55s</item>
- <item>117s</item>
- <item>Create initial surface 95s</item>
- <item>Topology correction: 121s</item>
- <item>Surface refinement: 98s</item>
- <item>Reduction of surface collisions with optimization: 84s</item>
- <item>Spherical mapping with areal smoothing 103s</item>
- <item>Spherical registration 323s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 35s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 56s</item>
- <item>117s</item>
- <item>Create initial surface 99s</item>
- <item>Topology correction: 126s</item>
- <item>Surface refinement: 94s</item>
- <item>Reduction of surface collisions with optimization: 79s</item>
- <item>Spherical mapping with areal smoothing 97s</item>
- <item>Spherical registration 284s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6003 0.6677 mm</item>
- <item>Surface intensity / position RMSE: 0.0786 / 0.0974</item>
- <item>Euler number / defect number / defect size: 52.0 / 27.0 / 2.98%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_57358/ds/sub-season214/surf/lh.thickness.sub-season214_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_57358/ds/sub-season214/surf/rh.thickness.sub-season214_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_57358/ds/sub-season214/sub-season214_ses-3_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1951s</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 10s</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 15s</item>
- <item>ROI estimation of 'mori' atlas 21s</item>
- <item>ROI estimation of 'anatomy3' atlas 32s</item>
- <item>ROI estimation of 'julichbrain' atlas 43s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 76s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 101s</item>
- <item>Write results 102s</item>
- <item>428s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_57358/ds/sub-season214/report/catreport_sub-season214_ses-3_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 60 minute(s) and 58 second(s).</item>
- <item>Image Quality Rating (IQR): 87.83% (B+)</item>
- <item>GM volume (GMV): 51.83% (737.75 / 1423.39 ml)</item>
- <item>GM thickness (GMT): 2.60 0.67 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_57358/ds/sub-season214/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_57358/ds/sub-season214/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_57358/ds/sub-season214/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|