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- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_57709/ds/sub-season117</path>
- <file>sub-season117_ses-3_acq-MPrageHiRes_T1w</file>
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- <F>/var/lib/condor/execute/dir_57709/ds/sub-season117/sub-season117_ses-3_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_57709/ds/sub-season117/mri/msub-season117_ses-3_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_57709/ds/sub-season117/mri/p0sub-season117_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season117/..son117_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>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>
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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>
- </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>
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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>
- <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>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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- <new_release>0</new_release>
- <lazy>0</lazy>
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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>
- </shooting>
- </regmethod>
- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_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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- </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>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.415792273939194</SurfaceDefectArea>
- <SurfaceDefectNumber>13.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0659656971693039</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0708039551973343</SurfacePositionRMSE>
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- <res_RMS>0.876668990040222</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.7790002822876 349.07568359375 924.050842285156 1322.38684082031]</tissue_mn>
- <tissue_mnr>[0.0073949615471065 0.263973951339722 0.698774933815002 0.999999940395355]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[32.3848077392162 163.632803614319 126.017253462663 70.8900605671987]</tissue_std>
- <tissue_stdr>[0.0246721114963293 0.124662362039089 0.0960052534937859 0.0540070347487926]</tissue_stdr>
- <contrast>401.303680419922</contrast>
- <contrastr>0.303469181060791</contrastr>
- <NCR>0.102763414382935</NCR>
- <ICR>0.295623272657394</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.75999495642906 1.74999998539232 1.75000000618539]</res_vx_vol>
- <res_RMS>1.75333798008044</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>3.53129577636719</contrastr>
- <NCR>1.80625057220459</NCR>
- <ICR>1.19301402568817</ICR>
- <SurfaceEulerNumber>1.91836734693878</SurfaceEulerNumber>
- <SurfaceDefectArea>1.1039480684848</SurfaceDefectArea>
- <SurfaceDefectNumber>1.675</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.31931400299072</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.41607904434204</SurfacePositionRMSE>
- <IQR>1.78116775803497</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>20220712-175728</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.415792273939194</SurfaceDefectArea>
- <SurfaceDefectNumber>13.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0659656971693039</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0708039551973343</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>20</EC_abs>
- <defect_size>0.415792273939194</defect_size>
- <vol_abs_CGW>[228.630712632356 773.156513294986 635.696181597981 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.01909811507512</vol_abs_WMH>
- <vol_rel_WMH>0.000622356300156499</vol_rel_WMH>
- <surf_TSA>2172.62477033171</surf_TSA>
- <vol_TIV>1637.48340752532</vol_TIV>
- <vol_rel_CGW>[0.139623224016589 0.472161433662056 0.388215342321354 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.52953319162661 0.625522681398271]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.51588988304138 0.814094144826674 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.93315772975661 0.258381650712872 0.302509877360861;2.55043574121434 0.178656490936907 0.434158540205997;3.22481696939364 0.29781899472532 0.263331582433142]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.814583467608341 0.36198456938876 0.50954954954955;4.2691575202059 0.361058746788359 0.49045045045045]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.23194211869383</vol_TIV>
- <vol_rel_CGW>[0.5 6.3297671275513 4.82211462502432 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.06223563001565</vol_rel_WMH>
- <surf_TSA>8.62384430269628</surf_TSA>
- <SQR>5.24626524505344</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.207451616014753 1 1 7838.83034749512 0.34638025712689]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00652296468615532 0 0.252866685390472]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[950.315491994778 559.240122888292 338.046606033728 1107.9319297884 2509.21525802792 5134.3788038557]</SPMvols0>
- <SPMvols1>[851.226946352875 531.532043406942 209.438380687006 1390.19077970018 2263.12997352771 4645.34086744512]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[436.767211914062 956.711975097656 1308.95520019531]</T3th>
- <Tth>
- <T3th>[0 0 19.2380771636963 436.767211914062 956.711975097656 1308.95520019531 1745.04919433594 3778.30859375]</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>[0.0194970611482859 0.0684942081570625 0.0748492032289505 0 0]</dtc>
- <ll>[0.0795331132941458 0 0.0795331132941458 0;0.187436803334615 0.00933177073319562 0.196768574067811 1989.9814453125;0.187436803334615 0.00933177073319562 0.196768574067811 1989.9814453125]</ll>
- <rmsdtc>[0.0414024665951729 0.0889216363430023 0.0989398211240768]</rmsdtc>
- <rmsgdt>[0.029555169865489 0.0413021817803383 0.0510010942816734]</rmsgdt>
- <rmsdt>0.0989398211240768</rmsdt>
- <dt>0.0748492032289505</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>[0.00939894467592239 0.0342903286218643 0.0484150461852551 0.0571182295680046 0.0636992901563644 0.0716866627335548]</dtc>
- <ll>[0.0823604408110521 0 0.0823604408110521 0;0.217413018925519 0.0127114392551893 0.230124458180708 6506.66796875;0.196851483649015 0.0160753374700575 0.212926821119073 11569.61328125;0.17636848877185 0.0186180158218427 0.194986504593692 20075.28515625;0.159185388826612 0.0218853435563034 0.181070732382915 38285.19140625;0.159185388826612 0.0218853435563034 0.181070732382915 38285.19140625]</ll>
- <rmsdtc>[0.0108541585505009 0.0392010100185871 0.0590683631598949 0.0844663307070732 0.109380297362804 0.117669641971588]</rmsdtc>
- <rmsgdt>[0.00329788541421294 0.0126481130719185 0.0281205475330353 0.0491769313812256 0.0695087015628815 0.075212374329567]</rmsgdt>
- <rmsdt>0.117669641971588</rmsdt>
- <dt>0.0716866627335548</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season117_ses-3_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 31s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 9s</item>
- <item>Estimate background 11s</item>
- <item>Initial correction 32s</item>
- <item>Refine background 5s</item>
- <item>Final correction 21s</item>
- <item>Final scaling 12s</item>
- <item>99s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 18s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 125s</item>
- <item>SPM preprocessing 1 (estimate 2): 111s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 26s</item>
- <item>Update Segmentation 33s</item>
- <item>Update Skull-Stripping 67s</item>
- <item>Update probability maps 13s</item>
- <item>139s</item>
- <item>Global intensity correction: 24s</item>
- <item>SANLM denoising after intensity normalization (medium): 15s</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 = 1.06) 27s</item>
- <item>Estimate local tissue thresholds (WM) 35s</item>
- <item>Estimate local tissue thresholds (GM) 49s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 39s</item>
- <item>167s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 13s</item>
- <item>Major structures 7s</item>
- <item>Ventricle detection 24s</item>
- <item>Blood vessel detection 20s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 56s</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>136s</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) 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>22s</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 | 0.0824 0.0000 0.0824 | 32.0000</item>
- <item>2 | 2.50 | 0.0798 0.0012 0.0810 | 29.4886</item>
- <item>3 | 2.50 | 0.0791 0.0017 0.0808 | 26.9772</item>
- <item>4 | 2.50 | 0.0787 0.0020 0.0806 | 24.6107</item>
- <item>5 | 2.50 | 0.0784 0.0021 0.0805 | 22.6548</item>
- <item>6 | 2.50 | 0.0781 0.0022 0.0803 | 20.6989</item>
- <item>7 | 2.50 | 0.0779 0.0023 0.0801 | 18.9688</item>
- <item>8 | 2.50 | 0.0776 0.0024 0.0799 | 17.4455</item>
- <item>9 | 2.50 | 0.0773 0.0024 0.0797 | 15.9223</item>
- <item>10 | 2.50 | 0.0770 0.0025 0.0795 | 14.6627</item>
- <item>11 | 2.50 | 0.0767 0.0026 0.0793 | 13.4764</item>
- <item>12 | 2.50 | 0.0764 0.0027 0.0790 | 12.3015</item>
- <item>13 | 2.50 | 0.0761 0.0028 0.0788 | 11.3776</item>
- <item>14 | 2.50 | 0.0757 0.0028 0.0786 | 10.4537</item>
- <item>15 | 2.25 | 0.0753 0.0029 0.0782 | 9.5920</item>
- <item>16 | 2.25 | 0.0725 0.0042 0.0767 | 8.8725</item>
- <item>29 | 2.00 | 0.0737 0.0019 0.0757 | 3.3283</item>
- <item>30 | 2.00 | 0.0677 0.0043 0.0721 | 3.1221</item>
- <item>31 | 2.00 | 0.0656 0.0054 0.0710 | 2.9160</item>
- <item>43 | 1.75 | 0.0646 0.0031 0.0677 | 1.5785</item>
- <item>44 | 1.75 | 0.0603 0.0054 0.0656 | 1.5194</item>
- <item>45 | 1.75 | 0.0588 0.0062 0.0650 | 1.4626</item>
- <item>57 | 1.50 | 0.0574 0.0045 0.0619 | 1.0900</item>
- <item>58 | 1.50 | 0.0541 0.0066 0.0607 | 1.0730</item>
- <item>59 | 1.50 | 0.0531 0.0073 0.0604 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 185s</item>
- <item>Prepare output 16s</item>
- <item>201s</item>
- <item>Jacobian determinant (RMS): 0.011 0.039 0.059 0.084 0.109 | 0.117670</item>
- <item>Template Matching: 0.082 0.217 0.197 0.176 0.159 | 0.159185</item>
- <item>Write result maps: 40s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 47s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 60s</item>
- <item>136s</item>
- <item>Create initial surface 109s</item>
- <item>Topology correction: 121s</item>
- <item>Surface refinement: 89s</item>
- <item>Reduction of surface collisions with optimization: 86s</item>
- <item>Spherical mapping with areal smoothing 98s</item>
- <item>Spherical registration 294s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 47s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 51s</item>
- <item>121s</item>
- <item>Create initial surface 90s</item>
- <item>Topology correction: 105s</item>
- <item>Surface refinement: 81s</item>
- <item>Reduction of surface collisions with optimization: 75s</item>
- <item>Spherical mapping with areal smoothing 93s</item>
- <item>Spherical registration 282s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5296 0.6254 mm</item>
- <item>Surface intensity / position RMSE: 0.0660 / 0.0708</item>
- <item>Euler number / defect number / defect size: 20.0 / 13.5 / 0.42%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_57709/ds/sub-season117/surf/lh.thickness.sub-season117_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_57709/ds/sub-season117/surf/rh.thickness.sub-season117_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_57709/ds/sub-season117/sub-season117_ses-3_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1896s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 10s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 35s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 24s</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 21s</item>
- <item>ROI estimation of 'anatomy3' atlas 30s</item>
- <item>ROI estimation of 'julichbrain' atlas 39s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s</item>
- <item>Write results 95s</item>
- <item>395s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_57709/ds/sub-season117/report/catreport_sub-season117_ses-3_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 60 minute(s) and 51 second(s).</item>
- <item>Image Quality Rating (IQR): 87.19% (B+)</item>
- <item>GM volume (GMV): 47.22% (773.16 / 1637.48 ml)</item>
- <item>GM thickness (GMT): 2.53 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_57709/ds/sub-season117/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|