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- <filedata>
- <path>/var/lib/condor/execute/dir_52325/ds/sub-f5416zj</path>
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- <F>/var/lib/condor/execute/dir_52325/ds/sub-f5416zj/sub-f5416zj_ses-wave1bas_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_52325/ds/sub-f5416zj/mri/msub-f5416zj_ses-wave1bas_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_52325/ds/sub-f5416zj/mri/p0sub-f5416zj_ses-wave1bas_T1w.nii</Fp0>
- <fnames>../ds/sub-f5416zj/sub-f5416zj_ses-wave1bas_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>
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- <accstr>0.5</accstr>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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- <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>
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- </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>
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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>
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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/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>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- </atlas>
- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
- <new_release>0</new_release>
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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>
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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>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.104986701094497</SurfaceDefectArea>
- <SurfaceDefectNumber>5.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.061244048178196</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0569396317005157</SurfacePositionRMSE>
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- <res_RMS>0.799999556619276</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[18.9629993438721 262.798950195312 721.717224121094 915.073181152344]</tissue_mn>
- <tissue_mnr>[0.020722933113575 0.28718900680542 0.78869891166687 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[57.2797656549519 112.147288407557 94.3346655800609 52.6253297845971]</tissue_std>
- <tissue_stdr>[0.0639204531908035 0.125148996710777 0.105271279811859 0.0587264075875282]</tissue_stdr>
- <contrast>197.447647094727</contrast>
- <contrastr>0.215772524476051</contrastr>
- <NCR>0.150123402476311</NCR>
- <ICR>1.08138883113861</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.59999718443049 1.60000006698447 1.60000008829895]</res_vx_vol>
- <res_RMS>1.59999911323855</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>4.84674549102783</contrastr>
- <NCR>2.48612403869629</NCR>
- <ICR>3.14183735847473</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.02624667527362</SurfaceDefectArea>
- <SurfaceDefectNumber>1.275</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.2248809337616</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.13879263401031</SurfacePositionRMSE>
- <IQR>2.28806624157606</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>20220711-105551</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.104986701094497</SurfaceDefectArea>
- <SurfaceDefectNumber>5.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.061244048178196</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0569396317005157</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.104986701094497</defect_size>
- <vol_abs_CGW>[295.00708552113 606.901784236704 503.030371024021 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.30000799736746</vol_abs_WMH>
- <vol_rel_WMH>0.000925312611130432</vol_rel_WMH>
- <surf_TSA>1779.66662770692</surf_TSA>
- <vol_TIV>1404.93924078185</vol_TIV>
- <vol_rel_CGW>[0.209978536407708 0.43197724614693 0.358044217445362 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.49158794908852 0.648407487670613]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.51325583457947 0.824336878378341 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.79777595897217 0.294241127786803 0.258318450336585;2.50185632224765 0.190134407850611 0.45092732518203;3.17972266965391 0.298466365089723 0.290754224481385]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.72097936180798 0.28562371515781 0.570743904980204;4.19048739116169 0.340737045486131 0.429256095019796]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00058121491506</vol_TIV>
- <vol_rel_CGW>[1.6210225647936 5.60806835752389 4.28024815814228 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.09253126111304</vol_rel_WMH>
- <surf_TSA>8.57446337089878</surf_TSA>
- <SQR>4.64901384973284</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.163900190304487 1 1 8547.94917948099 0.445283272737266]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0251209326088428 0.0178751517087221 0.310957551002502]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[715.690611933559 481.60906361548 397.753429801655 1078.04192299981 2258.38225527792 5879.48434790513]</SPMvols0>
- <SPMvols1>[627.32179800477 453.935975570917 284.345584738835 1570.83310620021 2069.46679197388 5217.71008517388]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[325.028106689453 742.615783691406 963.019714355469]</T3th>
- <Tth>
- <T3th>[0 0 20.9664611816406 325.028106689453 742.615783691406 963.019714355469 1282.01550292969 2470.02465820312]</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>[0.0247436575591564 0.0924890860915184 0.102900318801403 0 0]</dtc>
- <ll>[0.0870901583289566 0 0.0870901583289566 0;0.187929828913987 0.0130659014093919 0.200995730323379 2786.27734375;0.187929828913987 0.0130659014093919 0.200995730323379 2786.27734375]</ll>
- <rmsdtc>[0.0523802451789379 0.117075808346272 0.129228740930557]</rmsdtc>
- <rmsgdt>[0.0370582677423954 0.0504202954471111 0.0613768734037876]</rmsgdt>
- <rmsdt>0.129228740930557</rmsdt>
- <dt>0.102900318801403</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>[0.0126456925645471 0.048160046339035 0.0690376162528992 0.077890932559967 0.0830915719270706 0.0947043597698212]</dtc>
- <ll>[0.0870659925029023 0 0.0870659925029023 0;0.216182677045177 0.0188254235347985 0.235008100579976 9636.263671875;0.185677157147581 0.0209646358543417 0.206641793001923 15088.5;0.163492229928998 0.0211914729075781 0.184683702836576 22850.171875;0.146508184025751 0.0228553338720087 0.16936351789776 39982.046875;0.146508184025751 0.0228553338720087 0.16936351789776 39982.046875]</ll>
- <rmsdtc>[0.0145308393985033 0.0539001561701298 0.0798868909478188 0.109133161604404 0.132780954241753 0.14026315510273]</rmsdtc>
- <rmsgdt>[0.00387857062742114 0.0153839569538832 0.0319764502346516 0.052620317786932 0.0707783102989197 0.0757923796772957]</rmsgdt>
- <rmsdt>0.14026315510273</rmsdt>
- <dt>0.0947043597698212</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./ds/sub-f5416zj/sub-f5416zj_ses-wave1bas_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 166s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 14s</item>
- <item>Estimate background 13s</item>
- <item>Initial correction 16s</item>
- <item>Refine background 7s</item>
- <item>Final correction 13s</item>
- <item>Final scaling 15s</item>
- <item>93s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 20s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 164s</item>
- <item>SPM preprocessing 1 (estimate 2): 63s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 34s</item>
- <item>Update Segmentation 39s</item>
- <item>Update Skull-Stripping 91s</item>
- <item>Update probability maps 18s</item>
- <item>183s</item>
- <item>Global intensity correction: 36s</item>
- <item>SANLM denoising after intensity normalization (medium): 29s</item>
- <item>Fast Optimized Shooting registration 51s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 10s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.04) 34s</item>
- <item>Estimate local tissue thresholds (WM) 42s</item>
- <item>Estimate local tissue thresholds (GM) 60s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 59s</item>
- <item>215s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 15s</item>
- <item>Major structures 7s</item>
- <item>Ventricle detection 29s</item>
- <item>Blood vessel detection 25s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 60s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 4s</item>
- <item>Side alignment 8s</item>
- <item>Final corrections 9s</item>
- <item>157s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 64s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 10s</item>
- <item>Level 1 cleanup (brain masking) 6s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
- <item>26s</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 | 0.0871 0.0000 0.0871 | 32.0000</item>
- <item>2 | 2.50 | 0.0830 0.0016 0.0846 | 29.4886</item>
- <item>3 | 2.50 | 0.0817 0.0025 0.0842 | 26.9772</item>
- <item>4 | 2.50 | 0.0811 0.0028 0.0840 | 24.6107</item>
- <item>5 | 2.50 | 0.0807 0.0030 0.0837 | 22.6548</item>
- <item>6 | 2.50 | 0.0802 0.0032 0.0834 | 20.6989</item>
- <item>7 | 2.50 | 0.0798 0.0033 0.0831 | 18.9688</item>
- <item>8 | 2.50 | 0.0794 0.0035 0.0828 | 17.4455</item>
- <item>9 | 2.50 | 0.0789 0.0036 0.0825 | 15.9223</item>
- <item>10 | 2.50 | 0.0784 0.0037 0.0822 | 14.6627</item>
- <item>11 | 2.50 | 0.0780 0.0039 0.0818 | 13.4764</item>
- <item>12 | 2.50 | 0.0775 0.0040 0.0814 | 12.3015</item>
- <item>13 | 2.50 | 0.0770 0.0041 0.0811 | 11.3776</item>
- <item>14 | 2.50 | 0.0765 0.0042 0.0807 | 10.4537</item>
- <item>15 | 2.25 | 0.0759 0.0044 0.0803 | 9.5920</item>
- <item>16 | 2.25 | 0.0721 0.0063 0.0783 | 8.8725</item>
- <item>29 | 2.00 | 0.0720 0.0028 0.0748 | 3.3283</item>
- <item>30 | 2.00 | 0.0645 0.0058 0.0703 | 3.1221</item>
- <item>31 | 2.00 | 0.0619 0.0070 0.0689 | 2.9160</item>
- <item>43 | 1.75 | 0.0602 0.0041 0.0642 | 1.5785</item>
- <item>44 | 1.75 | 0.0559 0.0063 0.0622 | 1.5194</item>
- <item>45 | 1.75 | 0.0545 0.0071 0.0616 | 1.4626</item>
- <item>57 | 1.50 | 0.0525 0.0052 0.0578 | 1.0900</item>
- <item>58 | 1.50 | 0.0497 0.0071 0.0568 | 1.0730</item>
- <item>59 | 1.50 | 0.0488 0.0076 0.0565 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 199s</item>
- <item>Prepare output 20s</item>
- <item>219s</item>
- <item>Jacobian determinant (RMS): 0.015 0.054 0.080 0.109 0.133 | 0.140263</item>
- <item>Template Matching: 0.087 0.216 0.186 0.163 0.147 | 0.146508</item>
- <item>Write result maps: 117s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 59s</item>
- <item>CSF distance: 19s</item>
- <item>PBT2x thickness: 54s</item>
- <item>140s</item>
- <item>Create initial surface 94s</item>
- <item>Topology correction: 90s</item>
- <item>Surface refinement: 112s</item>
- <item>Reduction of surface collisions with optimization: 81s</item>
- <item>Spherical mapping with areal smoothing 96s</item>
- <item>Spherical registration 352s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 52s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 50s</item>
- <item>126s</item>
- <item>Create initial surface 103s</item>
- <item>Topology correction: 89s</item>
- <item>Surface refinement: 89s</item>
- <item>Reduction of surface collisions with optimization: 69s</item>
- <item>Spherical mapping with areal smoothing 104s</item>
- <item>Spherical registration 326s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4918 0.6483 mm</item>
- <item>Surface intensity / position RMSE: 0.0612 / 0.0569</item>
- <item>Euler number / defect number / defect size: 8.0 / 5.5 / 0.10%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/surf/lh.thickness.sub-f5416zj_ses-wave1bas_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/surf/rh.thickness.sub-f5416zj_ses-wave1bas_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/sub-f5416zj_ses-wave1bas_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 2032s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 19s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 68s</item>
- <item>ROI estimation of 'lpba40' atlas 19s</item>
- <item>ROI estimation of 'hammers' atlas 44s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 16s</item>
- <item>ROI estimation of 'aal3' atlas 24s</item>
- <item>ROI estimation of 'mori' atlas 34s</item>
- <item>ROI estimation of 'anatomy3' atlas 48s</item>
- <item>ROI estimation of 'julichbrain' atlas 66s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 50s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 123s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 175s</item>
- <item>Write results 177s</item>
- <item>717s</item>
- <item>Quality check: 11s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_52325/ds/sub-f5416zj/report/catreport_sub-f5416zj_ses-wave1bas_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 76 minute(s) and 11 second(s).</item>
- <item>Image Quality Rating (IQR): 82.12% (B-)</item>
- <item>GM volume (GMV): 43.20% (606.90 / 1404.94 ml)</item>
- <item>GM thickness (GMT): 2.49 0.65 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_52325/ds/sub-f5416zj/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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