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- <filedata>
- <path>/var/lib/condor/execute/dir_2524/ds/sub-season133</path>
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- <F>/var/lib/condor/execute/dir_2524/ds/sub-season133/sub-season133_ses-1_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_2524/ds/sub-season133/mri/msub-season133_ses-1_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_2524/ds/sub-season133/mri/p0sub-season133_ses-1_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season133/..son133_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>20</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <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>
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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/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>
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- <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>
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- <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>
- </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>
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- <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>
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- <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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- </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>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.347799333515903</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.067007452249527</SurfaceIntensityRMSE>
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- <res_RMS>0.876667794706029</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.89999961853027 338.52587890625 835.833068847656 1196.31494140625]</tissue_mn>
- <tissue_mnr>[0.00827541295439005 0.282973885536194 0.698673129081726 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[45.9928250609318 144.893697447586 110.465659842175 60.7505235454318]</tissue_std>
- <tissue_stdr>[0.038766223937273 0.122127339243889 0.0931087955832481 0.0512051247060299]</tissue_stdr>
- <contrast>363.489898681641</contrast>
- <contrastr>0.303841322660446</contrastr>
- <NCR>0.104362457990646</NCR>
- <ICR>0.290324121713638</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.75998781063886 1.74999994649519 1.75000004599035]</res_vx_vol>
- <res_RMS>1.75333558941206</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>3.5257134437561</contrastr>
- <NCR>1.82920551300049</NCR>
- <ICR>1.17987132072449</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.08694983337898</SurfaceDefectArea>
- <SurfaceDefectNumber>1.65</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.34014904499054</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.32510709762573</SurfacePositionRMSE>
- <IQR>1.79407015335332</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>20220712-174839</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.347799333515903</SurfaceDefectArea>
- <SurfaceDefectNumber>13</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.067007452249527</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0662553533911705</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.347799333515903</defect_size>
- <vol_abs_CGW>[212.907389852926 702.337436952142 503.265085289626 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.884506091409389</vol_abs_WMH>
- <vol_rel_WMH>0.000623545936385634</vol_rel_WMH>
- <surf_TSA>1899.4422760421</surf_TSA>
- <vol_TIV>1418.50991209469</vol_TIV>
- <vol_rel_CGW>[0.150092282075441 0.495123390371668 0.35478432755289 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.67131278065478 0.593125939126943]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.69169664382935 0.756115412552145 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.10228577056436 0.249830871094432 0.290817115607681;2.70570309632674 0.170988132559678 0.420389225415646;3.3153457768741 0.2728275035554 0.288793658976672]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.926892465116977 0.428061307437047 0.585674157303371;4.19048851950694 0.298339363053255 0.414325842696629]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00815847802069</vol_TIV>
- <vol_rel_CGW>[0.545479203941113 6.74215859144519 4.22170128507346 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.06235459363856</vol_rel_WMH>
- <surf_TSA>8.61323475038412</surf_TSA>
- <SQR>5.52962548301967</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.330853462219238 1 1 6618.27719207567 0.325772643949603]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00489453366026282 0 0.152128949761391]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[819.351273642754 453.446640194202 286.041154368924 359.561133492342 2448.87607249231 6063.88872086598]</SPMvols0>
- <SPMvols1>[742.515566483408 430.151895106776 182.539909276009 325.56198058984 1391.37780155083 6818.61727967354]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[369.835205078125 872.634887695312 1175.04040527344]</T3th>
- <Tth>
- <T3th>[0 0 15.1138410568237 369.835205078125 872.634887695312 1175.04040527344 1577.64306640625 3119.92822265625]</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>[0.021063631400466 0.0722240433096886 0.0788925066590309 0 0]</dtc>
- <ll>[0.079927033069087 0 0.079927033069087 0;0.185996432264312 0.00961391407759393 0.195610346341906 2050.14794921875;0.185996432264312 0.00961391407759393 0.195610346341906 2050.14794921875]</ll>
- <rmsdtc>[0.0450720153748989 0.0920954868197441 0.101490363478661]</rmsdtc>
- <rmsgdt>[0.0322760492563248 0.0414084233343601 0.0511582270264626]</rmsgdt>
- <rmsdt>0.101490363478661</rmsdt>
- <dt>0.0788925066590309</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>[0.00998751912266016 0.0361307226121426 0.0497201532125473 0.0569916926324368 0.0625716745853424 0.0703501999378204]</dtc>
- <ll>[0.0805918405220892 0 0.0805918405220892 0;0.209334691697192 0.0129397664835165 0.222274458180708 6623.54296875;0.186839883522854 0.0158863037945213 0.202726187317375 11433.5634765625;0.166405455905375 0.0178299312464758 0.18423538715185 19225.515625;0.149764111002754 0.0202082569955864 0.16997236799834 35351.375;0.149764111002754 0.0202082569955864 0.16997236799834 35351.375]</ll>
- <rmsdtc>[0.0114069702103734 0.0408399254083633 0.0597776584327221 0.0839634016156197 0.108092419803143 0.115520589053631]</rmsdtc>
- <rmsgdt>[0.0032385908998549 0.012529531493783 0.0274369083344936 0.0483385249972343 0.0667614787817001 0.0721267610788345]</rmsgdt>
- <rmsdt>0.115520589053631</rmsdt>
- <dt>0.0703501999378204</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season133_ses-1_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 67s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 11s</item>
- <item>Estimate background 11s</item>
- <item>Initial correction 22s</item>
- <item>Refine background 6s</item>
- <item>Final correction 16s</item>
- <item>Final scaling 13s</item>
- <item>90s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 16s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 123s</item>
- <item>SPM preprocessing 1 (estimate 2): 111s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 27s</item>
- <item>Update Segmentation 32s</item>
- <item>Update Skull-Stripping 72s</item>
- <item>Update probability maps 14s</item>
- <item>146s</item>
- <item>Global intensity correction: 28s</item>
- <item>SANLM denoising after intensity normalization (medium): 12s</item>
- <item>Fast Optimized Shooting registration 49s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 8s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.00) 26s</item>
- <item>Estimate local tissue thresholds (WM) 30s</item>
- <item>Estimate local tissue thresholds (GM) 39s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 34s</item>
- <item>147s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 15s</item>
- <item>Major structures 6s</item>
- <item>Ventricle detection 22s</item>
- <item>Blood vessel detection 16s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 45s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 8s</item>
- <item>121s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 63s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05]</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 | 0.0806 0.0000 0.0806 | 32.0000</item>
- <item>2 | 2.50 | 0.0781 0.0011 0.0793 | 29.4886</item>
- <item>3 | 2.50 | 0.0774 0.0017 0.0791 | 26.9772</item>
- <item>4 | 2.50 | 0.0770 0.0019 0.0790 | 24.6107</item>
- <item>5 | 2.50 | 0.0767 0.0021 0.0788 | 22.6548</item>
- <item>6 | 2.50 | 0.0765 0.0022 0.0787 | 20.6989</item>
- <item>7 | 2.50 | 0.0762 0.0023 0.0785 | 18.9688</item>
- <item>8 | 2.50 | 0.0759 0.0024 0.0783 | 17.4455</item>
- <item>9 | 2.50 | 0.0757 0.0024 0.0781 | 15.9223</item>
- <item>10 | 2.50 | 0.0754 0.0025 0.0779 | 14.6627</item>
- <item>11 | 2.50 | 0.0751 0.0026 0.0777 | 13.4764</item>
- <item>12 | 2.50 | 0.0748 0.0027 0.0774 | 12.3015</item>
- <item>13 | 2.50 | 0.0745 0.0028 0.0772 | 11.3776</item>
- <item>14 | 2.50 | 0.0742 0.0028 0.0770 | 10.4537</item>
- <item>15 | 2.25 | 0.0728 0.0029 0.0756 | 9.5920</item>
- <item>16 | 2.25 | 0.0698 0.0043 0.0741 | 8.8725</item>
- <item>29 | 2.00 | 0.0704 0.0020 0.0724 | 3.3283</item>
- <item>30 | 2.00 | 0.0644 0.0043 0.0687 | 3.1221</item>
- <item>31 | 2.00 | 0.0623 0.0053 0.0676 | 2.9160</item>
- <item>43 | 1.75 | 0.0610 0.0031 0.0641 | 1.5785</item>
- <item>44 | 1.75 | 0.0569 0.0052 0.0621 | 1.5194</item>
- <item>45 | 1.75 | 0.0555 0.0059 0.0614 | 1.4626</item>
- <item>57 | 1.50 | 0.0537 0.0043 0.0580 | 1.0900</item>
- <item>58 | 1.50 | 0.0509 0.0062 0.0570 | 1.0730</item>
- <item>59 | 1.50 | 0.0499 0.0067 0.0567 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 230s</item>
- <item>Prepare output 14s</item>
- <item>244s</item>
- <item>Jacobian determinant (RMS): 0.011 0.041 0.060 0.084 0.108 | 0.115521</item>
- <item>Template Matching: 0.081 0.209 0.187 0.166 0.150 | 0.149764</item>
- <item>Write result maps: 46s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 42s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 56s</item>
- <item>123s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 109s</item>
- <item>Surface refinement: 88s</item>
- <item>Reduction of surface collisions with optimization: 84s</item>
- <item>Spherical mapping with areal smoothing 97s</item>
- <item>Spherical registration 272s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 52s</item>
- <item>CSF distance: 19s</item>
- <item>PBT2x thickness: 56s</item>
- <item>135s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 116s</item>
- <item>Surface refinement: 88s</item>
- <item>Reduction of surface collisions with optimization: 90s</item>
- <item>Spherical mapping with areal smoothing 100s</item>
- <item>Spherical registration 269s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6714 0.5931 mm</item>
- <item>Surface intensity / position RMSE: 0.0670 / 0.0663</item>
- <item>Euler number / defect number / defect size: 12.0 / 13.0 / 0.35%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2524/ds/sub-season133/surf/lh.thickness.sub-season133_ses-1_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2524/ds/sub-season133/surf/rh.thickness.sub-season133_ses-1_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2524/ds/sub-season133/sub-season133_ses-1_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1880s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 19s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 66s</item>
- <item>ROI estimation of 'lpba40' atlas 19s</item>
- <item>ROI estimation of 'hammers' atlas 46s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 16s</item>
- <item>ROI estimation of 'aal3' atlas 27s</item>
- <item>ROI estimation of 'mori' atlas 40s</item>
- <item>ROI estimation of 'anatomy3' atlas 57s</item>
- <item>ROI estimation of 'julichbrain' atlas 76s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 28s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 123s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 180s</item>
- <item>Write results 181s</item>
- <item>739s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2524/ds/sub-season133/report/catreport_sub-season133_ses-1_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 68 minute(s) and 7 second(s).</item>
- <item>Image Quality Rating (IQR): 87.06% (B+)</item>
- <item>GM volume (GMV): 49.51% (702.34 / 1418.51 ml)</item>
- <item>GM thickness (GMT): 2.67 0.59 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2524/ds/sub-season133/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|