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- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_21555/ds/sub-season111</path>
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- <F>/var/lib/condor/execute/dir_21555/ds/sub-season111/sub-season111_ses-1_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_21555/ds/sub-season111/mri/msub-season111_ses-1_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_21555/ds/sub-season111/mri/p0sub-season111_ses-1_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season111/..son111_ses-1_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>
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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>
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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>
- </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>
- <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_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>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.215989325999584</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0616380721330643</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0603869967162609</SurfacePositionRMSE>
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- <res_RMS>0.876670942884145</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[11.5649995803833 340.918365478516 870.381713867188 1234.83911132812]</tissue_mn>
- <tissue_mnr>[0.00936559215188026 0.27608323097229 0.704854309558868 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[6.07939667125965 133.413165248958 114.840802820537 66.1707066840129]</tissue_std>
- <tissue_stdr>[0.00496977427974343 0.109062358736992 0.0938798561692238 0.0540931113064289]</tissue_stdr>
- <contrast>367.903015136719</contrast>
- <contrastr>0.297935992479324</contrastr>
- <NCR>0.106684632599354</NCR>
- <ICR>0.333870500326157</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.76000668484948 1.74999994249649 1.7499999930617]</res_vx_vol>
- <res_RMS>1.75334188576829</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>3.61429333686829</contrastr>
- <NCR>1.86254143714905</NCR>
- <ICR>1.28787326812744</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0539973314999</SurfaceDefectArea>
- <SurfaceDefectNumber>1.7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.23276138305664</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.20773994922638</SurfacePositionRMSE>
- <IQR>1.81366225940123</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>20220712-171434</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.215989325999584</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0616380721330643</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0603869967162609</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>0.215989325999584</defect_size>
- <vol_abs_CGW>[327.854572324633 745.764699654852 598.209428313723 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.776030810156327</vol_abs_WMH>
- <vol_rel_WMH>0.000464180815905497</vol_rel_WMH>
- <surf_TSA>2154.34286777318</surf_TSA>
- <vol_TIV>1671.82870029321</vol_TIV>
- <vol_rel_CGW>[0.196105361911261 0.446077220425788 0.357817417662951 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.55225130011473 0.60626944525869]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.56242346763611 0.716435883167847 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.97964252839574 0.237102633779991 0.309645416779448;2.58871173680527 0.171210510611201 0.409871370906053;3.2003832226778 0.254265923810059 0.2804832123145]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.920319492608026 0.379923663134423 0.55584872471416;4.09482879492316 0.311794915432797 0.44415127528584]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.57197888920357</vol_TIV>
- <vol_rel_CGW>[1.37186354007294 5.86130065419878 4.27617488618805 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04641808159055</vol_rel_WMH>
- <surf_TSA>8.6237863856614</surf_TSA>
- <SQR>4.83965238321911</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.0296556609017508 1 10892 9597.41417819258 0.33106802614096]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00716424500569701 0.00372157525271177 0.275203615427017]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[897.8769874105 531.426218497235 503.149606751102 1073.18994629652 2005.62774630334 5412.88333296044]</SPMvols0>
- <SPMvols1>[804.524119212374 504.195001181952 315.81593827804 801.29078608884 1824.23101605607 5640.69492807813]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[398.505004882812 897.412780761719 1208.98815917969]</T3th>
- <Tth>
- <T3th>[0 0 34.2084884643555 398.505004882812 897.412780761719 1208.98815917969 1614.22973632812 3140.55126953125]</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>[0.021722624078393 0.0814946368336678 0.089623898267746 0 0]</dtc>
- <ll>[0.0826883243531788 0 0.0826883243531788 0;0.188117367308251 0.0108510082652446 0.198968375573496 2313.95581054688;0.188117367308251 0.0108510082652446 0.198968375573496 2313.95581054688]</ll>
- <rmsdtc>[0.0490392260253429 0.102868095040321 0.1129195317626]</rmsdtc>
- <rmsgdt>[0.035261943936348 0.0447059720754623 0.0542695783078671]</rmsgdt>
- <rmsdt>0.1129195317626</rmsdt>
- <dt>0.089623898267746</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>[0.0106361601501703 0.0402546040713787 0.0573398806154728 0.0648076236248016 0.0699439272284508 0.0777257531881332]</dtc>
- <ll>[0.0831197706973867 0 0.0831197706973867 0;0.213945833333333 0.0144046331272894 0.228350466460623 7373.37158203125;0.190440868187553 0.0170934014881994 0.207534269675752 12302.326171875;0.169867491110777 0.0185830495749217 0.188450540685699 20037.58203125;0.152776019191095 0.0208870771615277 0.173663096352623 36538.87109375;0.152776019191095 0.0208870771615277 0.173663096352623 36538.87109375]</ll>
- <rmsdtc>[0.0122112203389406 0.0450149774551392 0.0657950714230537 0.0880898460745811 0.106095239520073 0.112344138324261]</rmsdtc>
- <rmsgdt>[0.0033873813226819 0.0132008092477918 0.0271659418940544 0.0451498553156853 0.0599251687526703 0.0647284537553787]</rmsgdt>
- <rmsdt>0.112344138324261</rmsdt>
- <dt>0.0777257531881332</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season111_ses-1_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 50s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 13s</item>
- <item>Refine background 4s</item>
- <item>Final correction 11s</item>
- <item>Final scaling 10s</item>
- <item>63s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 19s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 104s</item>
- <item>SPM preprocessing 1 (estimate 2): 103s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 20s</item>
- <item>Update Segmentation 26s</item>
- <item>Update Skull-Stripping 56s</item>
- <item>Update probability maps 11s</item>
- <item>113s</item>
- <item>Global intensity correction: 21s</item>
- <item>SANLM denoising after intensity normalization (medium): 36s</item>
- <item>Fast Optimized Shooting registration 36s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 7s</item>
- <item>Prepare partitions 6s</item>
- <item>Prepare segments (LASmod = 1.00) 24s</item>
- <item>Estimate local tissue thresholds (WM) 25s</item>
- <item>Estimate local tissue thresholds (GM) 35s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 40s</item>
- <item>141s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 6s</item>
- <item>Ventricle detection 27s</item>
- <item>Blood vessel detection 16s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.10) 46s</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>119s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 52s</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>18s</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 | 0.0831 0.0000 0.0831 | 32.0000</item>
- <item>2 | 2.50 | 0.0803 0.0012 0.0815 | 29.4886</item>
- <item>3 | 2.50 | 0.0795 0.0019 0.0813 | 26.9772</item>
- <item>4 | 2.50 | 0.0790 0.0021 0.0812 | 24.6107</item>
- <item>5 | 2.50 | 0.0787 0.0023 0.0810 | 22.6548</item>
- <item>6 | 2.50 | 0.0784 0.0024 0.0808 | 20.6989</item>
- <item>7 | 2.50 | 0.0781 0.0025 0.0806 | 18.9688</item>
- <item>8 | 2.50 | 0.0777 0.0026 0.0804 | 17.4455</item>
- <item>9 | 2.50 | 0.0774 0.0027 0.0802 | 15.9223</item>
- <item>10 | 2.50 | 0.0771 0.0029 0.0799 | 14.6627</item>
- <item>11 | 2.50 | 0.0767 0.0030 0.0797 | 13.4764</item>
- <item>12 | 2.50 | 0.0764 0.0030 0.0794 | 12.3015</item>
- <item>13 | 2.50 | 0.0760 0.0032 0.0791 | 11.3776</item>
- <item>14 | 2.50 | 0.0756 0.0032 0.0789 | 10.4537</item>
- <item>15 | 2.25 | 0.0741 0.0033 0.0775 | 9.5920</item>
- <item>16 | 2.25 | 0.0713 0.0048 0.0761 | 8.8725</item>
- <item>29 | 2.00 | 0.0719 0.0022 0.0740 | 3.3283</item>
- <item>30 | 2.00 | 0.0656 0.0047 0.0703 | 3.1221</item>
- <item>31 | 2.00 | 0.0635 0.0057 0.0692 | 2.9160</item>
- <item>43 | 1.75 | 0.0621 0.0033 0.0654 | 1.5785</item>
- <item>44 | 1.75 | 0.0580 0.0054 0.0634 | 1.5194</item>
- <item>45 | 1.75 | 0.0566 0.0062 0.0628 | 1.4626</item>
- <item>57 | 1.50 | 0.0548 0.0045 0.0593 | 1.0900</item>
- <item>58 | 1.50 | 0.0519 0.0064 0.0583 | 1.0730</item>
- <item>59 | 1.50 | 0.0509 0.0070 0.0579 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 158s</item>
- <item>Prepare output 13s</item>
- <item>170s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.066 0.088 0.106 | 0.112344</item>
- <item>Template Matching: 0.083 0.214 0.190 0.170 0.153 | 0.152776</item>
- <item>Write result maps: 30s</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: 18s</item>
- <item>PBT2x thickness: 49s</item>
- <item>116s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 97s</item>
- <item>Surface refinement: 112s</item>
- <item>Reduction of surface collisions with optimization: 74s</item>
- <item>Spherical mapping with areal smoothing 83s</item>
- <item>Spherical registration 273s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 52s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 46s</item>
- <item>121s</item>
- <item>Create initial surface 90s</item>
- <item>Topology correction: 97s</item>
- <item>Surface refinement: 81s</item>
- <item>Reduction of surface collisions with optimization: 72s</item>
- <item>Spherical mapping with areal smoothing 75s</item>
- <item>Spherical registration 267s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5522 0.6063 mm</item>
- <item>Surface intensity / position RMSE: 0.0616 / 0.0604</item>
- <item>Euler number / defect number / defect size: 14.0 / 14.0 / 0.22%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_21555/ds/sub-season111/surf/lh.thickness.sub-season111_ses-1_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_21555/ds/sub-season111/surf/rh.thickness.sub-season111_ses-1_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_21555/ds/sub-season111/sub-season111_ses-1_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1754s</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 14s</item>
- <item>ROI estimation of 'mori' atlas 20s</item>
- <item>ROI estimation of 'anatomy3' atlas 29s</item>
- <item>ROI estimation of 'julichbrain' atlas 38s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 15s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 66s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 92s</item>
- <item>Write results 92s</item>
- <item>392s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_21555/ds/sub-season111/report/catreport_sub-season111_ses-1_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 55 minute(s) and 59 second(s).</item>
- <item>Image Quality Rating (IQR): 86.86% (B+)</item>
- <item>GM volume (GMV): 44.61% (745.76 / 1671.83 ml)</item>
- <item>GM thickness (GMT): 2.55 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_21555/ds/sub-season111/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|