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- <filedata>
- <path>/var/lib/condor/execute/dir_21558/ds/sub-season212</path>
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- <Fp0>/var/lib/condor/execute/dir_21558/ds/sub-season212/mri/p0sub-season212_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season212/..son212_ses-3_acq-MPrageHiRes_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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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>32</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>
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- <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>
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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>
- </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_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>
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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>
- <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>
- </restypes>
- <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>
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- </shootingtpms>
- <templates>
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- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
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- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.226538283643712</SurfaceDefectArea>
- <SurfaceDefectNumber>9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0653772205114365</SurfaceIntensityRMSE>
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- <res_RMS>0.876671535336443</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[10.1969995498657 352.195953369141 891.980346679688 1276.03308105469]</tissue_mn>
- <tissue_mnr>[0.00799117144197226 0.276008486747742 0.699025988578796 0.999999940395355]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[60.9023908215524 149.137807897646 116.808640160827 69.9152596687615]</tissue_std>
- <tissue_stdr>[0.0481123812496662 0.117817617952824 0.0922778472304344 0.0552324689924717]</tissue_stdr>
- <contrast>387.146514892578</contrast>
- <contrastr>0.303398489952087</contrastr>
- <NCR>0.105553537607193</NCR>
- <ICR>0.304346352815628</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.76001023625939 1.74999998645801 1.74999993888257]</res_vx_vol>
- <res_RMS>1.75334307067289</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>3.53235602378845</contrastr>
- <NCR>1.84630393981934</NCR>
- <ICR>1.21464872360229</ICR>
- <SurfaceEulerNumber>1.40816326530612</SurfaceEulerNumber>
- <SurfaceDefectArea>1.05663457091093</SurfaceDefectArea>
- <SurfaceDefectNumber>1.45</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.30754446983337</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.34463167190552</SurfacePositionRMSE>
- <IQR>1.80399772048627</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>20220712-165706</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.226538283643712</SurfaceDefectArea>
- <SurfaceDefectNumber>9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0653772205114365</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0672315806150436</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>10</EC_abs>
- <defect_size>0.226538283643712</defect_size>
- <vol_abs_CGW>[241.274899975695 637.199208831852 466.08561176692 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.66759498397157</vol_abs_WMH>
- <vol_rel_WMH>0.000496515680007385</vol_rel_WMH>
- <surf_TSA>1845.64434396159</surf_TSA>
- <vol_TIV>1344.55972057447</vol_TIV>
- <vol_rel_CGW>[0.179445283302559 0.473909190556152 0.346645526141289 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.48373690302407 0.584786852561]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.47500443458557 0.72795775674316 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95344983817355 0.23367798695356 0.317995798433962;2.51808628858894 0.163493997973336 0.425203939650233;3.13142829297953 0.257199209410607 0.256800261915805]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.879039252914676 0.384509950095317 0.543551797040169;4.08664781056714 0.374962416350402 0.456448202959831]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.07287854338237</vol_TIV>
- <vol_rel_CGW>[1.07265235816378 6.36115643958607 4.07553028270992 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04965156800074</vol_rel_WMH>
- <surf_TSA>8.60209166728092</surf_TSA>
- <SQR>5.22017012147098</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.321450165339879 1 1 6711.36692838983 0.328867072662899]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00480932230129838 0 0.133892446756363]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[752.775698368573 417.352224237149 358.864407596899 659.992427016285 2795.22513610863 5374.36991269194]</SPMvols0>
- <SPMvols1>[675.93697392823 394.667166010067 231.285568554089 1235.09455662482 2487.27975779839 4866.52728084565]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[408.505401611328 932.708312988281 1250.69226074219]</T3th>
- <Tth>
- <T3th>[0 0 16.3114070892334 408.505401611328 932.708312988281 1250.69226074219 1671.78564453125 2771.2392578125]</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>[0.0225661508738995 0.0790926516056061 0.0868369042873383 0 0]</dtc>
- <ll>[0.0820429184857537 0 0.0820429184857537 0;0.188601343857856 0.010277095533648 0.198878439391504 2191.57006835938;0.188601343857856 0.010277095533648 0.198878439391504 2191.57006835938]</ll>
- <rmsdtc>[0.0484030358493328 0.100680738687515 0.110068581998348]</rmsdtc>
- <rmsgdt>[0.0346037410199642 0.0425038896501064 0.0521467551589012]</rmsgdt>
- <rmsdt>0.110068581998348</rmsdt>
- <dt>0.0868369042873383</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>[0.0109973233193159 0.0403511971235275 0.0560033544898033 0.0629944875836372 0.0682965740561485 0.0763769671320915]</dtc>
- <ll>[0.0820411969661159 0 0.0820411969661159 0;0.211833134920635 0.0141121088980464 0.225945243818681 7223.6357421875;0.189065817299142 0.0166812656052004 0.205747082904342 12005.70703125;0.168693839541414 0.0182526525948462 0.186946492136261 19681.32421875;0.15177404160281 0.0206098563654677 0.172383897968277 36053.9140625;0.15177404160281 0.0206098563654677 0.172383897968277 36053.9140625]</ll>
- <rmsdtc>[0.012692766264081 0.0455619730055332 0.066173754632473 0.0892980545759201 0.109430931508541 0.115099236369133]</rmsdtc>
- <rmsgdt>[0.00335668353363872 0.0128912515938282 0.0274451803416014 0.0465543791651726 0.0626792535185814 0.0672394558787346]</rmsgdt>
- <rmsdt>0.115099236369133</rmsdt>
- <dt>0.0763769671320915</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season212_ses-3_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 50s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 11s</item>
- <item>Refine background 4s</item>
- <item>Final correction 9s</item>
- <item>Final scaling 9s</item>
- <item>57s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 13s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 95s</item>
- <item>SPM preprocessing 1 (estimate 2): 98s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 21s</item>
- <item>Update Segmentation 25s</item>
- <item>Update Skull-Stripping 56s</item>
- <item>Update probability maps 11s</item>
- <item>113s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 21s</item>
- <item>Fast Optimized Shooting registration 37s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.03) 20s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 32s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 30s</item>
- <item>118s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 10s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 26s</item>
- <item>Blood vessel detection 12s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 38s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 5s</item>
- <item>Final corrections 5s</item>
- <item>104s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 41s</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) 6s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>14s</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 | 0.0820 0.0000 0.0820 | 32.0000</item>
- <item>2 | 2.50 | 0.0793 0.0012 0.0805 | 29.4886</item>
- <item>3 | 2.50 | 0.0785 0.0019 0.0804 | 26.9772</item>
- <item>4 | 2.50 | 0.0781 0.0021 0.0802 | 24.6107</item>
- <item>5 | 2.50 | 0.0778 0.0023 0.0800 | 22.6548</item>
- <item>6 | 2.50 | 0.0775 0.0024 0.0799 | 20.6989</item>
- <item>7 | 2.50 | 0.0772 0.0025 0.0797 | 18.9688</item>
- <item>8 | 2.50 | 0.0769 0.0026 0.0795 | 17.4455</item>
- <item>9 | 2.50 | 0.0766 0.0027 0.0792 | 15.9223</item>
- <item>10 | 2.50 | 0.0762 0.0028 0.0790 | 14.6627</item>
- <item>11 | 2.50 | 0.0759 0.0029 0.0788 | 13.4764</item>
- <item>12 | 2.50 | 0.0756 0.0030 0.0785 | 12.3015</item>
- <item>13 | 2.50 | 0.0752 0.0031 0.0783 | 11.3776</item>
- <item>14 | 2.50 | 0.0749 0.0032 0.0780 | 10.4537</item>
- <item>15 | 2.25 | 0.0735 0.0032 0.0767 | 9.5920</item>
- <item>16 | 2.25 | 0.0706 0.0047 0.0753 | 8.8725</item>
- <item>29 | 2.00 | 0.0715 0.0021 0.0736 | 3.3283</item>
- <item>30 | 2.00 | 0.0652 0.0045 0.0697 | 3.1221</item>
- <item>31 | 2.00 | 0.0630 0.0056 0.0686 | 2.9160</item>
- <item>43 | 1.75 | 0.0617 0.0032 0.0650 | 1.5785</item>
- <item>44 | 1.75 | 0.0576 0.0053 0.0630 | 1.5194</item>
- <item>45 | 1.75 | 0.0562 0.0061 0.0623 | 1.4626</item>
- <item>57 | 1.50 | 0.0544 0.0044 0.0589 | 1.0900</item>
- <item>58 | 1.50 | 0.0515 0.0063 0.0578 | 1.0730</item>
- <item>59 | 1.50 | 0.0506 0.0069 0.0575 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 163s</item>
- <item>Prepare output 12s</item>
- <item>175s</item>
- <item>Jacobian determinant (RMS): 0.013 0.046 0.066 0.089 0.109 | 0.115099</item>
- <item>Template Matching: 0.082 0.212 0.189 0.169 0.152 | 0.151774</item>
- <item>Write result maps: 29s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 36s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 38s</item>
- <item>93s</item>
- <item>Create initial surface 73s</item>
- <item>Topology correction: 88s</item>
- <item>Surface refinement: 65s</item>
- <item>Reduction of surface collisions with optimization: 60s</item>
- <item>Spherical mapping with areal smoothing 72s</item>
- <item>Spherical registration 300s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 52s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 41s</item>
- <item>114s</item>
- <item>Create initial surface 80s</item>
- <item>Topology correction: 89s</item>
- <item>Surface refinement: 83s</item>
- <item>Reduction of surface collisions with optimization: 57s</item>
- <item>Spherical mapping with areal smoothing 70s</item>
- <item>Spherical registration 282s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4837 0.5847 mm</item>
- <item>Surface intensity / position RMSE: 0.0654 / 0.0672</item>
- <item>Euler number / defect number / defect size: 10.0 / 9.0 / 0.23%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_21558/ds/sub-season212/surf/lh.thickness.sub-season212_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_21558/ds/sub-season212/surf/rh.thickness.sub-season212_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_21558/ds/sub-season212/sub-season212_ses-3_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1619s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 34s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 24s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 8s</item>
- <item>ROI estimation of 'aal3' atlas 14s</item>
- <item>ROI estimation of 'mori' atlas 20s</item>
- <item>ROI estimation of 'anatomy3' atlas 30s</item>
- <item>ROI estimation of 'julichbrain' atlas 40s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 64s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 98s</item>
- <item>Write results 98s</item>
- <item>399s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_21558/ds/sub-season212/report/catreport_sub-season212_ses-3_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 52 minute(s) and 18 second(s).</item>
- <item>Image Quality Rating (IQR): 86.96% (B+)</item>
- <item>GM volume (GMV): 47.39% (637.20 / 1344.56 ml)</item>
- <item>GM thickness (GMT): 2.48 0.58 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_21558/ds/sub-season212/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|