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- <path>/var/lib/condor/execute/dir_10740/ds/sub-021</path>
- <file>sub-021_ses-01_acq-mprage_run-01_T1w</file>
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- <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>
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- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
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- <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>24</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>
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- <item>csf</item>
- <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/lpba40.nii</td>
- <td>0</td>
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- <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>
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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/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>
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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/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>
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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/aal3.nii</td>
- <td>1</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/mori.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/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>
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- <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>
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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/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- </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_400Parcels_17Networks_order.nii</td>
- <td>1</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/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <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>
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- <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>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
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- <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>
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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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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <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>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </shootingtpms>
- <templates>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>32</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0578441610779</SurfaceDefectArea>
- <SurfaceDefectNumber>16.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0667341947555542</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0698251277208328</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 79.9226913452148 316.907684326172 589.794860839844]</tissue_mn>
- <tissue_mnr>[0 0.135509297251701 0.537318468093872 0.999999940395355]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[1.48558597538856 60.5473706834881 70.4571164473112 48.3635700371201]</tissue_std>
- <tissue_stdr>[0.00251881801523268 0.102658353745937 0.119460374116898 0.0820006653666496]</tissue_stdr>
- <contrast>201.000350952148</contrast>
- <contrastr>0.340797036886215</contrastr>
- <NCR>0.146111994981766</NCR>
- <ICR>0.214870423078537</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.62399999971164 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.97137784957886</contrastr>
- <NCR>2.42853856086731</NCR>
- <ICR>0.99273419380188</ICR>
- <SurfaceEulerNumber>2.53061224489796</SurfaceEulerNumber>
- <SurfaceDefectArea>1.26446104026948</SurfaceDefectArea>
- <SurfaceDefectNumber>1.825</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.33468389511108</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.39650249481201</SurfacePositionRMSE>
- <IQR>2.28105303260273</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>20220711-133000</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>32</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0578441610779</SurfaceDefectArea>
- <SurfaceDefectNumber>16.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0667341947555542</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0698251277208328</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>32</EC_abs>
- <defect_size>1.0578441610779</defect_size>
- <vol_abs_CGW>[310.446164705882 720.309564705882 535.503078431373 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.495219607843137</vol_abs_WMH>
- <vol_rel_WMH>0.000316179934863443</vol_rel_WMH>
- <surf_TSA>2112.65442678452</surf_TSA>
- <vol_TIV>1566.25880784314</vol_TIV>
- <vol_rel_CGW>[0.198208727160099 0.459891788699855 0.341899484140046 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.3848463989841 0.585493051294606]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.36082696914673 0.70474656849062 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.81378644459394 0.236167915032062 0.299612973691709;2.38655315558471 0.16605469399122 0.440420505271156;3.01697274873669 0.259189869075693 0.259966521037136]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.880786058439668 0.296584290932272 0.476540858725762;3.98080358111762 0.388880500249101 0.523459141274238]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.63092800546552</vol_TIV>
- <vol_rel_CGW>[1.40963949640982 6.1094071246382 3.99029245941175 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03161799348634</vol_rel_WMH>
- <surf_TSA>8.62356828675244</surf_TSA>
- <SQR>5.01645481138082</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.492801400118096 101 32 5717.24 0.417664122796944]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.226209029555321]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[966.110152941176 489.566309803922 423.578498039216 468.986611764706 3745.77775686275 5887.88409019608]</SPMvols0>
- <SPMvols1>[822.847364705882 460.236588235294 234.920050980392 1670.78556470588 3406.28919215686 4677.1872627451]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[109.304397583008 332.335784912109 628.515014648438]</T3th>
- <Tth>
- <T3th>[0 0 5.07745218276978 109.304397583008 332.335784912109 628.515014648438 888.120361328125 1445.04931640625]</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>[0.0170126296579838 0.0602238364517689 0.0658096149563789 0 0]</dtc>
- <ll>[0.0831045369808079 0 0.0831045369808079 0;0.204394648484394 0.0086504648856613 0.213045113370055 1844.6943359375;0.204394648484394 0.0086504648856613 0.213045113370055 1844.6943359375]</ll>
- <rmsdtc>[0.039126068353653 0.0821652933955193 0.0918388813734055]</rmsdtc>
- <rmsgdt>[0.028416471555829 0.0412259362637997 0.0510255619883537]</rmsgdt>
- <rmsdt>0.0918388813734055</rmsdt>
- <dt>0.0658096149563789</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>[0.0096550052985549 0.0428896993398666 0.0503799244761467 0.059005293995142 0.0661153569817543 0.0746630430221558]</dtc>
- <ll>[0.0891935891279858 0 0.0891935891279858 0;0.224984554334554 0.0178136866605617 0.242798240995116 9118.380859375;0.213692030631697 0.0189527783227006 0.232644808954398 13640.5419921875;0.193716746563019 0.0205111924739305 0.21422793903695 22116.64453125;0.176790219012401 0.0237942702959323 0.200584489308333 41624.578125;0.176790219012401 0.0237942702959323 0.200584489308333 41624.578125]</ll>
- <rmsdtc>[0.0118510955944657 0.0426917858421803 0.0679278969764709 0.0914163291454315 0.116657048463821 0.123352721333504]</rmsdtc>
- <rmsgdt>[0.0034110730048269 0.0133081283420324 0.0299953576177359 0.0508410967886448 0.0705579668283463 0.0763132870197296]</rmsgdt>
- <rmsdt>0.123352721333504</rmsdt>
- <dt>0.0746630430221558</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-021/sub-021_ses-01_acq-mprage_run-01_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 42s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 5s</item>
- <item>Final correction 7s</item>
- <item>Final scaling 8s</item>
- <item>54s</item>
- <item>Correct center-of-mass 8s</item>
- <item>Affine registration 14s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 102s</item>
- <item>SPM preprocessing 1 (estimate 2): 96s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 24s</item>
- <item>Update Segmentation 27s</item>
- <item>Update Skull-Stripping 66s</item>
- <item>Update probability maps 12s</item>
- <item>128s</item>
- <item>Global intensity correction: 22s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 50s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 21s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 29s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 22s</item>
- <item>108s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 12s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 22s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 36s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 6s</item>
- <item>103s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 58s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.08,0.99 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 6s</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>16s</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 | 0.0892 0.0000 0.0892 | 32.0000</item>
- <item>2 | 2.50 | 0.0861 0.0013 0.0875 | 29.4886</item>
- <item>3 | 2.50 | 0.0853 0.0020 0.0873 | 26.9772</item>
- <item>4 | 2.50 | 0.0848 0.0022 0.0871 | 24.6107</item>
- <item>5 | 2.50 | 0.0845 0.0024 0.0869 | 22.6548</item>
- <item>6 | 2.50 | 0.0842 0.0025 0.0867 | 20.6989</item>
- <item>7 | 2.50 | 0.0839 0.0026 0.0865 | 18.9688</item>
- <item>8 | 2.50 | 0.0836 0.0027 0.0863 | 17.4455</item>
- <item>9 | 2.50 | 0.0832 0.0028 0.0860 | 15.9223</item>
- <item>10 | 2.50 | 0.0829 0.0029 0.0858 | 14.6627</item>
- <item>11 | 2.50 | 0.0825 0.0030 0.0856 | 13.4764</item>
- <item>12 | 2.50 | 0.0822 0.0031 0.0853 | 12.3015</item>
- <item>13 | 2.50 | 0.0818 0.0032 0.0850 | 11.3776</item>
- <item>14 | 2.50 | 0.0814 0.0033 0.0847 | 10.4537</item>
- <item>15 | 2.25 | 0.0822 0.0034 0.0855 | 9.5920</item>
- <item>16 | 2.25 | 0.0788 0.0050 0.0838 | 8.8725</item>
- <item>17 | 2.25 | 0.0775 0.0056 0.0831 | 8.1530</item>
- <item>18 | 2.25 | 0.0767 0.0058 0.0825 | 7.5234</item>
- <item>19 | 2.25 | 0.0760 0.0059 0.0820 | 6.9630</item>
- <item>20 | 2.25 | 0.0755 0.0059 0.0814 | 6.4027</item>
- <item>21 | 2.25 | 0.0750 0.0059 0.0809 | 5.9447</item>
- <item>29 | 2.00 | 0.0773 0.0035 0.0808 | 3.3283</item>
- <item>30 | 2.00 | 0.0728 0.0055 0.0784 | 3.1221</item>
- <item>31 | 2.00 | 0.0712 0.0063 0.0775 | 2.9160</item>
- <item>43 | 1.75 | 0.0706 0.0036 0.0742 | 1.5785</item>
- <item>44 | 1.75 | 0.0661 0.0060 0.0721 | 1.5194</item>
- <item>45 | 1.75 | 0.0646 0.0068 0.0714 | 1.4626</item>
- <item>57 | 1.50 | 0.0635 0.0050 0.0684 | 1.0900</item>
- <item>58 | 1.50 | 0.0601 0.0072 0.0673 | 1.0730</item>
- <item>59 | 1.50 | 0.0589 0.0079 0.0669 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 284s</item>
- <item>Prepare output 13s</item>
- <item>297s</item>
- <item>Jacobian determinant (RMS): 0.012 0.043 0.068 0.091 0.117 | 0.123353</item>
- <item>Template Matching: 0.089 0.225 0.214 0.194 0.177 | 0.176790</item>
- <item>Write result maps: 36s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 74s</item>
- <item>CSF distance: 25s</item>
- <item>PBT2x thickness: 70s</item>
- <item>178s</item>
- <item>Create initial surface 124s</item>
- <item>Topology correction: 140s</item>
- <item>Surface refinement: 137s</item>
- <item>Reduction of surface collisions with optimization: 116s</item>
- <item>Spherical mapping with areal smoothing 124s</item>
- <item>Spherical registration 315s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 53s</item>
- <item>CSF distance: 24s</item>
- <item>PBT2x thickness: 71s</item>
- <item>159s</item>
- <item>Create initial surface 121s</item>
- <item>Topology correction: 145s</item>
- <item>Surface refinement: 159s</item>
- <item>Reduction of surface collisions with optimization: 121s</item>
- <item>Spherical mapping with areal smoothing 125s</item>
- <item>Spherical registration 324s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3849 0.5853 mm</item>
- <item>Surface intensity / position RMSE: 0.0667 / 0.0698</item>
- <item>Euler number / defect number / defect size: 32.0 / 16.5 / 1.06%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_10740/ds/sub-021/surf/lh.thickness.sub-021_ses-01_acq-mprage_run-01_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_10740/ds/sub-021/surf/rh.thickness.sub-021_ses-01_acq-mprage_run-01_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_10740/ds/sub-021/sub-021_ses-01_acq-mprage_run-01_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 2421s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 17s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 63s</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 26s</item>
- <item>ROI estimation of 'mori' atlas 37s</item>
- <item>ROI estimation of 'anatomy3' atlas 52s</item>
- <item>ROI estimation of 'julichbrain' atlas 68s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 34s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 113s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 168s</item>
- <item>Write results 170s</item>
- <item>692s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_10740/ds/sub-021/report/catreport_sub-021_ses-01_acq-mprage_run-01_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 73 minute(s) and 19 second(s).</item>
- <item>Image Quality Rating (IQR): 82.19% (B-)</item>
- <item>GM volume (GMV): 45.99% (720.31 / 1566.26 ml)</item>
- <item>GM thickness (GMT): 2.38 0.59 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_10740/ds/sub-021/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_10740/ds/sub-021/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_10740/ds/sub-021/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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