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- <filedata>
- <path>/var/lib/condor/execute/dir_32760/ds/sub-season104</path>
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- <Fm>/var/lib/condor/execute/dir_32760/ds/sub-season104/mri/msub-season104_ses-3_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_32760/ds/sub-season104/mri/p0sub-season104_ses-3_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season104/..son104_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>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>
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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>
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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>
- </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>
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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>
- </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>
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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>
- <BS>13</BS>
- <VT>15</VT>
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- <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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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_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_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>46</SurfaceEulerNumber>
- <SurfaceDefectArea>1.16196024460311</SurfaceDefectArea>
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- <SurfaceIntensityRMSE>0.0763235986232758</SurfaceIntensityRMSE>
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- <res_RMS>0.876669120461051</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.78999996185303 302.745971679688 802.827880859375 1148.51831054688]</tissue_mn>
- <tissue_mnr>[0.00852402579039335 0.26359698176384 0.69901180267334 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[6.70594819052912 149.330649092976 105.973289897296 61.2159192729136]</tissue_std>
- <tissue_stdr>[0.00588898034766316 0.13113808631897 0.0930628404021263 0.0537581443786621]</tissue_stdr>
- <contrast>348.662445068359</contrast>
- <contrastr>0.303575873374939</contrastr>
- <NCR>0.104635879397392</NCR>
- <ICR>0.282553553581238</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.75999568575157 1.75000001450287 1.75000002760435]</res_vx_vol>
- <res_RMS>1.7533382409221</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>3.52969527244568</contrastr>
- <NCR>1.83313059806824</NCR>
- <ICR>1.16059911251068</ICR>
- <SurfaceEulerNumber>3.24489795918367</SurfaceEulerNumber>
- <SurfaceDefectArea>1.29049006115078</SurfaceDefectArea>
- <SurfaceDefectNumber>2</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.52647197246552</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.75082099437714</SurfacePositionRMSE>
- <IQR>1.79632620175696</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>20220712-181145</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>46</SurfaceEulerNumber>
- <SurfaceDefectArea>1.16196024460311</SurfaceDefectArea>
- <SurfaceDefectNumber>20</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0763235986232758</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0875410512089729</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>46</EC_abs>
- <defect_size>1.16196024460311</defect_size>
- <vol_abs_CGW>[212.098544891309 715.803603627002 509.637143571868 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.847485607439556</vol_abs_WMH>
- <vol_rel_WMH>0.00058953909093317</vol_rel_WMH>
- <surf_TSA>1973.89801389154</surf_TSA>
- <vol_TIV>1437.53929209018</vol_TIV>
- <vol_rel_CGW>[0.147542780957951 0.497936722540798 0.354520496501252 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.58950631703182 0.677847900096468]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.60617184638977 0.888444937973105 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.92677657068391 0.303184717415676 0.288702438060664;2.62311181064386 0.196626261080873 0.426429096207393;3.33743738831722 0.308526899597662 0.284868465731943]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.736483277634622 0.296710433594738 0.631981351981352;4.35802457300596 0.314306123966218 0.368018648018648]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.03350033547699</vol_TIV>
- <vol_rel_CGW>[0.5 6.79268539045973 4.21696294003685 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05895390909332</vol_rel_WMH>
- <surf_TSA>8.62023481969396</surf_TSA>
- <SQR>5.56999702002818</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.344181197030204 1 1 6486.48677835532 0.325845276057328]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00540917133912444 0 0.175522685050964]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[851.144079545271 448.217968024344 313.992400328435 507.676247841369 2347.85018262637 5959.03876826466]</SPMvols0>
- <SPMvols1>[762.201258218052 423.236245352578 202.610270877363 419.424034439048 1277.41466029951 6806.09186624533]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[360.190612792969 839.235900878906 1131.36694335938]</T3th>
- <Tth>
- <T3th>[0 0 14.9340295791626 360.190612792969 839.235900878906 1131.36694335938 1516.955078125 3403.9755859375]</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>[0.0195298101752996 0.0696083158254623 0.0760018825531006 0 0]</dtc>
- <ll>[0.0796609354190895 0 0.0796609354190895 0;0.188719585734685 0.0094931283060099 0.198212714040694 2024.390625;0.188719585734685 0.0094931283060099 0.198212714040694 2024.390625]</ll>
- <rmsdtc>[0.0431752502918243 0.0896026045084 0.0993525683879852]</rmsdtc>
- <rmsgdt>[0.0311007667332888 0.0423350296914577 0.0527384020388126]</rmsgdt>
- <rmsdt>0.0993525683879852</rmsdt>
- <dt>0.0760018825531006</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>[0.00904969125986099 0.0334925800561905 0.0462495721876621 0.0538092218339443 0.0600912496447563 0.0667325034737587]</dtc>
- <ll>[0.0800483654601945 0 0.0800483654601945 0;0.210790460927961 0.0123560916514042 0.223146552579365 6324.7744140625;0.191801785818494 0.0155664506470991 0.207368236465593 11203.361328125;0.172108113143066 0.0179078372908227 0.190015950433889 19309.51953125;0.155427374435005 0.0208940775175165 0.176321451952522 36551.1171875;0.155427374435005 0.0208940775175165 0.176321451952522 36551.1171875]</ll>
- <rmsdtc>[0.0104591455310583 0.0378563962876797 0.055602241307497 0.0776594579219818 0.100219286978245 0.107037216424942]</rmsdtc>
- <rmsgdt>[0.00316510233096778 0.0121225444599986 0.0269339960068464 0.0471972450613976 0.0662422552704811 0.0714925304055214]</rmsgdt>
- <rmsdt>0.107037216424942</rmsdt>
- <dt>0.0667325034737587</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season104_ses-3_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 37s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 11s</item>
- <item>Estimate background 12s</item>
- <item>Initial correction 11s</item>
- <item>Refine background 6s</item>
- <item>Final correction 10s</item>
- <item>Final scaling 12s</item>
- <item>73s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 17s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 8s</item>
- <item>Use initial fine affine registration. 141s</item>
- <item>SPM preprocessing 1 (estimate 2): 129s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 30s</item>
- <item>Update Segmentation 35s</item>
- <item>Update Skull-Stripping 75s</item>
- <item>Update probability maps 15s</item>
- <item>155s</item>
- <item>Global intensity correction: 29s</item>
- <item>SANLM denoising after intensity normalization (medium): 13s</item>
- <item>Fast Optimized Shooting registration 53s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 9s</item>
- <item>Prepare partitions 4s</item>
- <item>Prepare segments (LASmod = 1.03) 30s</item>
- <item>Estimate local tissue thresholds (WM) 31s</item>
- <item>Estimate local tissue thresholds (GM) 42s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 35s</item>
- <item>157s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 16s</item>
- <item>Major structures 8s</item>
- <item>Ventricle detection 29s</item>
- <item>Blood vessel detection 18s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 50s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 7s</item>
- <item>Final corrections 8s</item>
- <item>137s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 69s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 9s</item>
- <item>Level 1 cleanup (brain masking) 5s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
- <item>21s</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 | 0.0800 0.0000 0.0800 | 32.0000</item>
- <item>2 | 2.50 | 0.0778 0.0011 0.0789 | 29.4886</item>
- <item>3 | 2.50 | 0.0771 0.0016 0.0787 | 26.9772</item>
- <item>4 | 2.50 | 0.0768 0.0018 0.0786 | 24.6107</item>
- <item>5 | 2.50 | 0.0765 0.0019 0.0785 | 22.6548</item>
- <item>6 | 2.50 | 0.0763 0.0020 0.0783 | 20.6989</item>
- <item>7 | 2.50 | 0.0760 0.0021 0.0782 | 18.9688</item>
- <item>8 | 2.50 | 0.0758 0.0022 0.0780 | 17.4455</item>
- <item>9 | 2.50 | 0.0755 0.0023 0.0778 | 15.9223</item>
- <item>10 | 2.50 | 0.0752 0.0024 0.0776 | 14.6627</item>
- <item>11 | 2.50 | 0.0750 0.0024 0.0774 | 13.4764</item>
- <item>12 | 2.50 | 0.0747 0.0025 0.0772 | 12.3015</item>
- <item>13 | 2.50 | 0.0744 0.0026 0.0770 | 11.3776</item>
- <item>14 | 2.50 | 0.0741 0.0026 0.0768 | 10.4537</item>
- <item>15 | 2.25 | 0.0731 0.0027 0.0758 | 9.5920</item>
- <item>16 | 2.25 | 0.0703 0.0041 0.0744 | 8.8725</item>
- <item>29 | 2.00 | 0.0718 0.0019 0.0736 | 3.3283</item>
- <item>30 | 2.00 | 0.0659 0.0042 0.0702 | 3.1221</item>
- <item>31 | 2.00 | 0.0639 0.0052 0.0691 | 2.9160</item>
- <item>43 | 1.75 | 0.0630 0.0030 0.0660 | 1.5785</item>
- <item>44 | 1.75 | 0.0588 0.0052 0.0640 | 1.5194</item>
- <item>45 | 1.75 | 0.0574 0.0060 0.0633 | 1.4626</item>
- <item>57 | 1.50 | 0.0559 0.0043 0.0603 | 1.0900</item>
- <item>58 | 1.50 | 0.0528 0.0063 0.0592 | 1.0730</item>
- <item>59 | 1.50 | 0.0518 0.0070 0.0588 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 247s</item>
- <item>Prepare output 15s</item>
- <item>262s</item>
- <item>Jacobian determinant (RMS): 0.010 0.038 0.056 0.078 0.100 | 0.107037</item>
- <item>Template Matching: 0.080 0.211 0.192 0.172 0.155 | 0.155427</item>
- <item>Write result maps: 42s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 65s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 62s</item>
- <item>157s</item>
- <item>Create initial surface 111s</item>
- <item>Topology correction: 130s</item>
- <item>Surface refinement: 147s</item>
- <item>Reduction of surface collisions with optimization: 98s</item>
- <item>Spherical mapping with areal smoothing 109s</item>
- <item>Spherical registration 281s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 47s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 57s</item>
- <item>132s</item>
- <item>Create initial surface 102s</item>
- <item>Topology correction: 111s</item>
- <item>Surface refinement: 100s</item>
- <item>Reduction of surface collisions with optimization: 94s</item>
- <item>Spherical mapping with areal smoothing 97s</item>
- <item>Spherical registration 256s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5893 0.6774 mm</item>
- <item>Surface intensity / position RMSE: 0.0763 / 0.0875</item>
- <item>Euler number / defect number / defect size: 46.0 / 20.0 / 1.16%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/lh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_32760/ds/sub-season104/surf/rh.thickness.sub-season104_ses-3_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_32760/ds/sub-season104/sub-season104_ses-3_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 2046s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 18s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 66s</item>
- <item>ROI estimation of 'lpba40' atlas 19s</item>
- <item>ROI estimation of 'hammers' atlas 47s</item>
- <item>ROI estimation of 'thalamus' atlas 4s</item>
- <item>ROI estimation of 'ibsr' atlas 17s</item>
- <item>ROI estimation of 'aal3' atlas 27s</item>
- <item>ROI estimation of 'mori' atlas 40s</item>
- <item>ROI estimation of 'anatomy3' atlas 59s</item>
- <item>ROI estimation of 'julichbrain' atlas 77s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 37s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 124s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 186s</item>
- <item>Write results 187s</item>
- <item>751s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_32760/ds/sub-season104/report/catreport_sub-season104_ses-3_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 71 minute(s) and 47 second(s).</item>
- <item>Image Quality Rating (IQR): 87.04% (B+)</item>
- <item>GM volume (GMV): 49.79% (715.80 / 1437.54 ml)</item>
- <item>GM thickness (GMT): 2.59 0.68 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_32760/ds/sub-season104/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|