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- <filedata>
- <path>/var/lib/condor/execute/dir_9532/ds/sub-sc012</path>
- <file>sub-sc012_T1w</file>
- <fname>/var/lib/condor/execute/dir_9532/ds/sub-sc012/sub-sc012_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_9532/ds/sub-sc012/sub-sc012_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_9532/ds/sub-sc012/mri/msub-sc012_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_9532/ds/sub-sc012/mri/p0sub-sc012_T1w.nii</Fp0>
- <fnames>..32/ds/sub-sc012/sub-sc012_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>
- <samp>3</samp>
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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>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
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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>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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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>
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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>
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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>
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- <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>
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- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
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- <HC>19</HC>
- <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>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
- <darteltpms>
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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_2_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>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
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- <SurfacePositionRMSE>0.0639883577823639</SurfacePositionRMSE>
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- <tissue_mn>[0 34405.5390625 181500.71875 353441.9375]</tissue_mn>
- <tissue_mnr>[0 0.0973442420363426 0.513523459434509 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[6928.93810721181 37464.126441636 44446.8408858854 33976.0680867772]</tissue_std>
- <tissue_stdr>[0.0196041762828827 0.105997964739799 0.125754296779633 0.0961291342973709]</tissue_stdr>
- <contrast>118769.921875</contrast>
- <contrastr>0.336037993431091</contrastr>
- <NCR>0.127652615308762</NCR>
- <ICR>0.294857054948807</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000001020678 1.99999995504914 1.99999996687424]</res_vx_vol>
- <res_RMS>1.99999997737672</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[1.89584374427795 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>3.04276347160339</contrastr>
- <NCR>2.16354608535767</NCR>
- <ICR>1.19111371040344</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.07718655864885</SurfaceDefectArea>
- <SurfaceDefectNumber>1.325</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.30351400375366</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.27976715564728</SurfacePositionRMSE>
- <IQR>2.09285021498761</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>20220711-191253</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.308746234595399</SurfaceDefectArea>
- <SurfaceDefectNumber>6.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0651756972074509</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0639883577823639</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>0.308746234595399</defect_size>
- <vol_abs_CGW>[240.81163235643 713.905780220753 485.572327088234 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.548623478047935</vol_abs_WMH>
- <vol_rel_WMH>0.000380911883865382</vol_rel_WMH>
- <surf_TSA>1983.84094478235</surf_TSA>
- <vol_TIV>1440.28973966542</vol_TIV>
- <vol_rel_CGW>[0.167196658925287 0.495668170479778 0.337135170594935 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.55884719391862 0.601212776812941]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.55681610107422 0.755414574960239 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.04268338601155 0.241260417409607 0.322834596744128;2.60996340523327 0.16647305604417 0.422772461787001;3.23616582477783 0.265952317353721 0.25439294146887]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.89742624518666 0.355540945389583 0.594202898550725;4.17445249493633 0.337294857972064 0.405797101449275]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.03857631817599</vol_TIV>
- <vol_rel_CGW>[0.852669880123697 6.75194271695004 3.90472648338604 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03809118838654</vol_rel_WMH>
- <surf_TSA>8.62074690676507</surf_TSA>
- <SQR>5.53009351553291</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.710125078914141 1591 555 3673.29487534702 0.500699628972035]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.197280257940292]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[871.50376938751 419.755168544358 375.902741277409 758.361760372372 1735.78606886288 9109.66395888975]</SPMvols0>
- <SPMvols1>[785.192655899596 397.453500044074 221.896108637164 819.078350766328 1365.67434665114 9082.77914964208]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[44731.8828125 205372.421875 361548.96875]</T3th>
- <Tth>
- <T3th>[0 0 798.866943359375 44731.8828125 205372.421875 361548.96875 519957.5 938178.0625]</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>[0.0210165958851576 0.0776282846927643 0.0857344195246696 0 0]</dtc>
- <ll>[0.0820671286092562 0 0.0820671286092562 0;0.190051679851628 0.0107652886288793 0.200816968480507 2295.67626953125;0.190051679851628 0.0107652886288793 0.200816968480507 2295.67626953125]</ll>
- <rmsdtc>[0.0464679189026356 0.105209551751614 0.118805505335331]</rmsdtc>
- <rmsgdt>[0.0333072207868099 0.0555282421410084 0.0705264732241631]</rmsgdt>
- <rmsdt>0.118805505335331</rmsdt>
- <dt>0.0857344195246696</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>[0.0103442957624793 0.0388612896203995 0.0564240030944347 0.0655647739768028 0.072031632065773 0.0808181539177895]</dtc>
- <ll>[0.0838966032822781 0 0.0838966032822781 0;0.218361492673993 0.0144347765949328 0.232796269268926 7388.80126953125;0.195106883899393 0.0175124099661566 0.21261929386555 12603.8916015625;0.175220485879259 0.0192295175898335 0.194450003469092 20734.650390625;0.159263506993729 0.0219492421805376 0.181212749174266 38396.97265625;0.159263506993729 0.0219492421805376 0.181212749174266 38396.97265625]</ll>
- <rmsdtc>[0.0120760966092348 0.0451372675597668 0.0704749077558517 0.101467780768871 0.127498239278793 0.135442733764648]</rmsdtc>
- <rmsgdt>[0.0036438861861825 0.015179174952209 0.032828014343977 0.056995265185833 0.0782493874430656 0.0865670219063759]</rmsgdt>
- <rmsdt>0.135442733764648</rmsdt>
- <dt>0.0808181539177895</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./execute/dir_9532/ds/sub-sc012/sub-sc012_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 34s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 9s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 4s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>50s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 12s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 123s</item>
- <item>SPM preprocessing 1 (estimate 2): 85s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 25s</item>
- <item>Update Segmentation 24s</item>
- <item>Update Skull-Stripping 56s</item>
- <item>Update probability maps 12s</item>
- <item>118s</item>
- <item>Global intensity correction: 23s</item>
- <item>SANLM denoising after intensity normalization (medium): 15s</item>
- <item>Fast Optimized Shooting registration 45s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.00) 18s</item>
- <item>Estimate local tissue thresholds (WM) 27s</item>
- <item>Estimate local tissue thresholds (GM) 37s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 15s</item>
- <item>110s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 21s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 28s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 6s</item>
- <item>89s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.08,0.99 0.05]</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>15s</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 | 0.0839 0.0000 0.0839 | 32.0000</item>
- <item>2 | 2.50 | 0.0811 0.0012 0.0823 | 29.4886</item>
- <item>3 | 2.50 | 0.0803 0.0018 0.0821 | 26.9772</item>
- <item>4 | 2.50 | 0.0799 0.0021 0.0819 | 24.6107</item>
- <item>5 | 2.50 | 0.0795 0.0022 0.0818 | 22.6548</item>
- <item>6 | 2.50 | 0.0792 0.0023 0.0816 | 20.6989</item>
- <item>7 | 2.50 | 0.0789 0.0025 0.0814 | 18.9688</item>
- <item>8 | 2.50 | 0.0786 0.0026 0.0812 | 17.4455</item>
- <item>9 | 2.50 | 0.0783 0.0027 0.0809 | 15.9223</item>
- <item>10 | 2.50 | 0.0780 0.0028 0.0807 | 14.6627</item>
- <item>11 | 2.50 | 0.0776 0.0029 0.0805 | 13.4764</item>
- <item>12 | 2.50 | 0.0773 0.0029 0.0802 | 12.3015</item>
- <item>13 | 2.50 | 0.0769 0.0031 0.0800 | 11.3776</item>
- <item>14 | 2.50 | 0.0766 0.0031 0.0797 | 10.4537</item>
- <item>15 | 2.25 | 0.0758 0.0032 0.0790 | 9.5920</item>
- <item>16 | 2.25 | 0.0728 0.0048 0.0776 | 8.8725</item>
- <item>29 | 2.00 | 0.0735 0.0022 0.0756 | 3.3283</item>
- <item>30 | 2.00 | 0.0671 0.0048 0.0719 | 3.1221</item>
- <item>31 | 2.00 | 0.0650 0.0058 0.0709 | 2.9160</item>
- <item>43 | 1.75 | 0.0640 0.0034 0.0674 | 1.5785</item>
- <item>44 | 1.75 | 0.0598 0.0056 0.0654 | 1.5194</item>
- <item>45 | 1.75 | 0.0584 0.0064 0.0648 | 1.4626</item>
- <item>57 | 1.50 | 0.0571 0.0047 0.0618 | 1.0900</item>
- <item>58 | 1.50 | 0.0541 0.0067 0.0608 | 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: 223s</item>
- <item>Prepare output 15s</item>
- <item>238s</item>
- <item>Jacobian determinant (RMS): 0.012 0.045 0.070 0.101 0.127 | 0.135443</item>
- <item>Template Matching: 0.084 0.218 0.195 0.175 0.159 | 0.159264</item>
- <item>Write result maps: 44s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 63s</item>
- <item>129s</item>
- <item>Create initial surface 111s</item>
- <item>Topology correction: 117s</item>
- <item>Surface refinement: 101s</item>
- <item>Reduction of surface collisions with optimization: 88s</item>
- <item>Spherical mapping with areal smoothing 107s</item>
- <item>Spherical registration 350s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 36s</item>
- <item>CSF distance: 19s</item>
- <item>PBT2x thickness: 58s</item>
- <item>120s</item>
- <item>Create initial surface 132s</item>
- <item>Topology correction: 130s</item>
- <item>Surface refinement: 175s</item>
- <item>Reduction of surface collisions with optimization: 105s</item>
- <item>Spherical mapping with areal smoothing 121s</item>
- <item>Spherical registration 350s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5587 0.6006 mm</item>
- <item>Surface intensity / position RMSE: 0.0652 / 0.0640</item>
- <item>Euler number / defect number / defect size: 14.0 / 6.5 / 0.31%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_9532/ds/sub-sc012/surf/lh.thickness.sub-sc012_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_9532/ds/sub-sc012/surf/rh.thickness.sub-sc012_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_9532/ds/sub-sc012/sub-sc012_T1w.nii</item>
- <item>Surface ROI estimation: 129s</item>
- <item>Surface and thickness estimation takes: 2413s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 48s</item>
- <item>ROI estimation of 'lpba40' atlas 14s</item>
- <item>ROI estimation of 'hammers' atlas 34s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 23s</item>
- <item>ROI estimation of 'mori' atlas 33s</item>
- <item>ROI estimation of 'anatomy3' atlas 48s</item>
- <item>ROI estimation of 'julichbrain' atlas 63s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 25s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 45s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 100s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 149s</item>
- <item>Write results 150s</item>
- <item>612s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_9532/ds/sub-sc012/report/catreport_sub-sc012_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 70 minute(s) and 3 second(s).</item>
- <item>Image Quality Rating (IQR): 84.07% (B)</item>
- <item>GM volume (GMV): 49.57% (713.91 / 1440.29 ml)</item>
- <item>GM thickness (GMT): 2.56 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_9532/ds/sub-sc012/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_9532/ds/sub-sc012/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_9532/ds/sub-sc012/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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