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- <fnames>..s/sub-wlsubj062/.._ses-anat_acq-highres_run-01_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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- <biasreg>0.001</biasreg>
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- <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>20</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>
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- </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>
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- </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>
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- <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>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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- <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>
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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>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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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>
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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>
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- <item>gm</item>
- <item>wm</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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- <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>
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- <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>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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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>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.107512667052155</SurfaceDefectArea>
- <SurfaceDefectNumber>9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0656073987483978</SurfaceIntensityRMSE>
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- <res_vx_vol>[0.800000979164593 0.800000012737503 0.800000000197966]</res_vx_vol>
- <res_vx_voli>[0.800000981774701 0.800000011723598 0.800000002814389]</res_vx_voli>
- <res_RMS>0.800000330700152</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[4.73099994659424 141.200744628906 354.352783203125 500.7490234375]</tissue_mn>
- <tissue_mnr>[0.0094478465616703 0.281979084014893 0.70764547586441 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.92287214455975 60.8332095467636 48.1442110664035 24.5422119071891]</tissue_std>
- <tissue_stdr>[0.00790872890502214 0.122643142938614 0.0970614105463028 0.049478467553854]</tissue_stdr>
- <contrast>147.792556762695</contrast>
- <contrastr>0.295142978429794</contrastr>
- <NCR>0.11182851344347</NCR>
- <ICR>0.351380735635757</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.60000195832919 1.60000002547501 1.60000000039593]</res_vx_vol>
- <res_RMS>1.6000006614003</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>3.65618848800659</contrastr>
- <NCR>1.93638408184052</NCR>
- <ICR>1.33130145072937</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.02687816676304</SurfaceDefectArea>
- <SurfaceDefectNumber>1.45</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.31214797496796</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.21762883663177</SurfacePositionRMSE>
- <IQR>1.81985496339668</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>20220712-154406</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.107512667052155</SurfaceDefectArea>
- <SurfaceDefectNumber>9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0656073987483978</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0608814433217049</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.107512667052155</defect_size>
- <vol_abs_CGW>[310.58686121725 692.371609503589 544.219167239255 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.28397110492627</vol_abs_WMH>
- <vol_rel_WMH>0.000829879564843728</vol_rel_WMH>
- <surf_TSA>1999.30550502427</surf_TSA>
- <vol_TIV>1547.17763796009</vol_TIV>
- <vol_rel_CGW>[0.200744150895788 0.447506215521871 0.351749633582341 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.4957834551239 0.598641384627118]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.48022556304932 0.730969301160556 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.94577975079471 0.235003067179187 0.314105195079786;2.5278667654964 0.170577245606579 0.435170329465318;3.17265793759817 0.268510770239731 0.250724475454896]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.879132652758057 0.391966663315309 0.521300448430493;4.09187744880076 0.321603263739785 0.478699551569507]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.49899991655762</vol_TIV>
- <vol_rel_CGW>[1.45517512384677 5.88696507761981 4.1671988789932 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08298795648437</vol_rel_WMH>
- <surf_TSA>8.62141565916675</surf_TSA>
- <SQR>4.85109372950742</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.269232259114583 1 1 6896.39818438586 0.485750828576513]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00591114535927773 0.00460187764838338 0.0709441155195236]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[810.907447166072 500.851251519511 517.656692621377 643.94359951343 2246.22248507642 5305.60676415783]</SPMvols0>
- <SPMvols1>[713.27012625979 475.624010313539 323.380401856071 510.596932676286 1438.13699869538 5976.2629046721]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[144.395797729492 365.367004394531 494.275787353516]</T3th>
- <Tth>
- <T3th>[0 0 6.25316143035889 144.395797729492 365.367004394531 494.275787353516 669.2158203125 1713.88659667969]</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>[0.0210253410041332 0.074954979121685 0.0824093222618103 0 0]</dtc>
- <ll>[0.0840074982629771 0 0.0840074982629771 0;0.195546785608775 0.0102762792433868 0.205823064852162 2191.39599609375;0.195546785608775 0.0102762792433868 0.205823064852162 2191.39599609375]</ll>
- <rmsdtc>[0.0454724244773388 0.0976754203438759 0.107424378395081]</rmsdtc>
- <rmsgdt>[0.0322844609618187 0.0427724942564964 0.0524042658507824]</rmsgdt>
- <rmsdt>0.107424378395081</rmsdt>
- <dt>0.0824093222618103</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>[0.0101706478744745 0.0371848829090595 0.0518376566469669 0.0590775869786739 0.0644181743264198 0.072346106171608]</dtc>
- <ll>[0.0838821143871107 0 0.0838821143871107 0;0.215978952991453 0.0141520852411477 0.230131038232601 7244.0986328125;0.192496334471289 0.0165437458620601 0.209040080333349 11906.732421875;0.172613739854137 0.0180381818374677 0.190651921691605 19450.06640625;0.155716999370624 0.0205485301208504 0.176265529491475 35946.6328125;0.155716999370624 0.0205485301208504 0.176265529491475 35946.6328125]</ll>
- <rmsdtc>[0.0121109457686543 0.0438773483037949 0.0643630623817444 0.0879172757267952 0.109180927276611 0.115623809397221]</rmsdtc>
- <rmsgdt>[0.00334871048107743 0.0128687573596835 0.0273849479854107 0.0463164411485195 0.0633926466107368 0.0683046579360962]</rmsgdt>
- <rmsdt>0.115623809397221</rmsdt>
- <dt>0.072346106171608</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 68s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 13s</item>
- <item>Estimate background 11s</item>
- <item>Initial correction 13s</item>
- <item>Refine background 7s</item>
- <item>Final correction 12s</item>
- <item>Final scaling 13s</item>
- <item>82s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 17s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 157s</item>
- <item>SPM preprocessing 1 (estimate 2): 67s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 34s</item>
- <item>Update Segmentation 44s</item>
- <item>Update Skull-Stripping 99s</item>
- <item>Update probability maps 18s</item>
- <item>196s</item>
- <item>Global intensity correction: 33s</item>
- <item>SANLM denoising after intensity normalization (medium): 23s</item>
- <item>Fast Optimized Shooting registration 63s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 11s</item>
- <item>Prepare partitions 5s</item>
- <item>Prepare segments (LASmod = 1.01) 33s</item>
- <item>Estimate local tissue thresholds (WM) 38s</item>
- <item>Estimate local tissue thresholds (GM) 54s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 53s</item>
- <item>202s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 21s</item>
- <item>Major structures 9s</item>
- <item>Ventricle detection 27s</item>
- <item>Blood vessel detection 26s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.12) 70s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 5s</item>
- <item>Side alignment 10s</item>
- <item>Final corrections 10s</item>
- <item>177s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 59s</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) 10s</item>
- <item>Level 1 cleanup (brain masking) 6s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 6s</item>
- <item>25s</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 | 0.0810 0.0013 0.0822 | 29.4886</item>
- <item>3 | 2.50 | 0.0801 0.0019 0.0821 | 26.9772</item>
- <item>4 | 2.50 | 0.0797 0.0021 0.0819 | 24.6107</item>
- <item>5 | 2.50 | 0.0794 0.0023 0.0817 | 22.6548</item>
- <item>6 | 2.50 | 0.0791 0.0024 0.0815 | 20.6989</item>
- <item>7 | 2.50 | 0.0788 0.0025 0.0813 | 18.9688</item>
- <item>8 | 2.50 | 0.0785 0.0026 0.0811 | 17.4455</item>
- <item>9 | 2.50 | 0.0782 0.0027 0.0809 | 15.9223</item>
- <item>10 | 2.50 | 0.0778 0.0028 0.0807 | 14.6627</item>
- <item>11 | 2.50 | 0.0775 0.0029 0.0804 | 13.4764</item>
- <item>12 | 2.50 | 0.0772 0.0030 0.0801 | 12.3015</item>
- <item>13 | 2.50 | 0.0768 0.0031 0.0799 | 11.3776</item>
- <item>14 | 2.50 | 0.0765 0.0031 0.0796 | 10.4537</item>
- <item>15 | 2.25 | 0.0750 0.0032 0.0782 | 9.5920</item>
- <item>16 | 2.25 | 0.0720 0.0047 0.0767 | 8.8725</item>
- <item>29 | 2.00 | 0.0723 0.0021 0.0744 | 3.3283</item>
- <item>30 | 2.00 | 0.0662 0.0045 0.0707 | 3.1221</item>
- <item>31 | 2.00 | 0.0642 0.0055 0.0697 | 2.9160</item>
- <item>43 | 1.75 | 0.0629 0.0032 0.0660 | 1.5785</item>
- <item>44 | 1.75 | 0.0589 0.0053 0.0641 | 1.5194</item>
- <item>45 | 1.75 | 0.0575 0.0060 0.0636 | 1.4626</item>
- <item>57 | 1.50 | 0.0557 0.0044 0.0601 | 1.0900</item>
- <item>58 | 1.50 | 0.0528 0.0062 0.0591 | 1.0730</item>
- <item>59 | 1.50 | 0.0519 0.0068 0.0588 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 242s</item>
- <item>Prepare output 17s</item>
- <item>259s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.064 0.088 0.109 | 0.115624</item>
- <item>Template Matching: 0.084 0.216 0.192 0.173 0.156 | 0.155717</item>
- <item>Write result maps: 56s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 60s</item>
- <item>CSF distance: 22s</item>
- <item>PBT2x thickness: 63s</item>
- <item>153s</item>
- <item>Create initial surface 96s</item>
- <item>Topology correction: 111s</item>
- <item>Surface refinement: 93s</item>
- <item>Reduction of surface collisions with optimization: 73s</item>
- <item>Spherical mapping with areal smoothing 104s</item>
- <item>Spherical registration 304s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 69s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 59s</item>
- <item>158s</item>
- <item>Create initial surface 98s</item>
- <item>Topology correction: 110s</item>
- <item>Surface refinement: 128s</item>
- <item>Reduction of surface collisions with optimization: 72s</item>
- <item>Spherical mapping with areal smoothing 103s</item>
- <item>Spherical registration 290s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4958 0.5984 mm</item>
- <item>Surface intensity / position RMSE: 0.0656 / 0.0609</item>
- <item>Euler number / defect number / defect size: 8.0 / 9.0 / 0.11%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/surf/lh.thickness.sub-wlsubj062_ses-anat_acq-highres_run-01_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/surf/rh.thickness.sub-wlsubj062_ses-anat_acq-highres_run-01_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 2036s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 28s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 106s</item>
- <item>ROI estimation of 'lpba40' atlas 31s</item>
- <item>ROI estimation of 'hammers' atlas 75s</item>
- <item>ROI estimation of 'thalamus' atlas 5s</item>
- <item>ROI estimation of 'ibsr' atlas 26s</item>
- <item>ROI estimation of 'aal3' atlas 41s</item>
- <item>ROI estimation of 'mori' atlas 62s</item>
- <item>ROI estimation of 'anatomy3' atlas 90s</item>
- <item>ROI estimation of 'julichbrain' atlas 118s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 44s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 60s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 194s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 284s</item>
- <item>Write results 285s</item>
- <item>1167s</item>
- <item>Quality check: 11s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/report/catreport_sub-wlsubj062_ses-anat_acq-highres_run-01_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 81 minute(s) and 17 second(s).</item>
- <item>Image Quality Rating (IQR): 86.80% (B+)</item>
- <item>GM volume (GMV): 44.75% (692.37 / 1547.18 ml)</item>
- <item>GM thickness (GMT): 2.50 0.60 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2937729/ds/sub-wlsubj062/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|