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- <Fp0>/var/lib/condor/execute/dir_26479/ds/sub-002/mri/p0sub-002_ses-03_acq-PHILLIPS_run-1_T1w.nii</Fp0>
- <fnames>..6479/ds/sub-002/..02_ses-03_acq-PHILLIPS_run-1_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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- <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>
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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>
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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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- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
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- <VT>15</VT>
- <NV>17</NV>
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- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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- </darteltpms>
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- </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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- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.681757346707616</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0649838224053383</SurfaceIntensityRMSE>
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- <res_RMS>0.999999973772677</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 5431.86572265625 38243.94140625 74853.5234375]</tissue_mn>
- <tissue_mnr>[0 0.0725665986537933 0.510917067527771 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[158.806410641941 7935.84095584598 9121.44676059703 6730.04490127928]</tissue_std>
- <tissue_stdr>[0.00212156237103045 0.106018267571926 0.121857278048992 0.0899095237255096]</tissue_stdr>
- <contrast>25114.611328125</contrast>
- <contrastr>0.335516750812531</contrastr>
- <NCR>0.144846230745316</NCR>
- <ICR>0.278768330812454</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.9999999830283 1.9999999432068 1.99999991640096]</res_vx_vol>
- <res_RMS>1.99999994754535</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>3.05058193206787</contrastr>
- <NCR>2.41036796569824</NCR>
- <ICR>1.15121114253998</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.1704393366769</SurfaceDefectArea>
- <SurfaceDefectNumber>1.575</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.29967641830444</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.35734736919403</SurfacePositionRMSE>
- <IQR>2.26703186598457</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>20220712-194343</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.681757346707616</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0649838224053383</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0678673684597015</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.681757346707616</defect_size>
- <vol_abs_CGW>[334.357392293694 767.950582300191 556.652814621185 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.816399981183524</vol_abs_WMH>
- <vol_rel_WMH>0.000492115296811686</vol_rel_WMH>
- <surf_TSA>2068.16446284898</surf_TSA>
- <vol_TIV>1658.96078921507</vol_TIV>
- <vol_rel_CGW>[0.201546289983077 0.462910628926645 0.335543081090279 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.60680660218591 0.651979378139666]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.58931541442871 0.854124070150025 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.99092853249088 0.280961637158875 0.302633784269125;2.62959322915463 0.187709435693276 0.441458158745361;3.34866710625739 0.308470378881515 0.255908056985514]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.835131062485007 0.315967517042987 0.552675124103696;4.41125370767251 0.324713637187223 0.447324875896304]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.44141475144267</vol_TIV>
- <vol_rel_CGW>[1.46958135745468 6.16362480112508 3.87613292188001 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04921152968117</vol_rel_WMH>
- <surf_TSA>8.62310959641717</surf_TSA>
- <SQR>5.05565584037486</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.591877624511719 9350 3760 6686.67647387911 0.487819022936081]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.195875689387321]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[947.310578166282 511.365035272826 632.030095236823 1319.24414214294 5832.77050085978 7850.4949602374]</SPMvols0>
- <SPMvols1>[797.925338472074 485.561608416566 339.898098048344 838.932470860271 2770.74042241418 11151.0071312257]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[9475.5439453125 41123.5 76100.84375]</T3th>
- <Tth>
- <T3th>[0 0 240.455108642578 9475.5439453125 41123.5 76100.84375 109413.4921875 186408.609375]</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>[0.0192161966115236 0.0705761164426804 0.0773709267377853 0 0]</dtc>
- <ll>[0.0849352008869954 0 0.0849352008869954 0;0.206389226833311 0.00976740412351464 0.216156630956826 2082.87939453125;0.206389226833311 0.00976740412351464 0.216156630956826 2082.87939453125]</ll>
- <rmsdtc>[0.0411478467285633 0.0910965204238892 0.101772643625736]</rmsdtc>
- <rmsgdt>[0.0293787308037281 0.0425192639231682 0.0531069152057171]</rmsgdt>
- <rmsdt>0.101772643625736</rmsdt>
- <dt>0.0773709267377853</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>[0.00936010386794806 0.0351071879267693 0.0496225021779537 0.0576138310134411 0.0641141533851624 0.0717389807105064]</dtc>
- <ll>[0.0851795496715549 0 0.0851795496715549 0;0.224504777167277 0.0136817603403541 0.238186537507631 7003.35107421875;0.203052466646381 0.0169350020824302 0.219987468728811 12188.32421875;0.182043961310319 0.0191425602433801 0.201186521553699 20640.88671875;0.165037159452666 0.0222039591208864 0.187241118573553 38842.5625;0.165037159452666 0.0222039591208864 0.187241118573553 38842.5625]</ll>
- <rmsdtc>[0.0108417151495814 0.0401019901037216 0.0596835762262344 0.0836444199085236 0.10603442043066 0.113372772932053]</rmsdtc>
- <rmsgdt>[0.00320764654316008 0.0125556150451303 0.027555925771594 0.0477813221514225 0.0658526420593262 0.0718148350715637]</rmsgdt>
- <rmsdt>0.113372772932053</rmsdt>
- <dt>0.0717389807105064</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-002/sub-002_ses-03_acq-PHILLIPS_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 26s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 7s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 4s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 7s</item>
- <item>44s</item>
- <item>Correct center-of-mass 7s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 60s</item>
- <item>SPM preprocessing 1 (estimate 2): 69s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 20s</item>
- <item>Update Segmentation 18s</item>
- <item>Update Skull-Stripping 44s</item>
- <item>Update probability maps 10s</item>
- <item>93s</item>
- <item>Global intensity correction: 18s</item>
- <item>SANLM denoising after intensity normalization (medium): 6s</item>
- <item>Fast Optimized Shooting registration 30s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.01) 13s</item>
- <item>Estimate local tissue thresholds (WM) 19s</item>
- <item>Estimate local tissue thresholds (GM) 24s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 11s</item>
- <item>78s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 18s</item>
- <item>Blood vessel detection 9s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.06) 24s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 5s</item>
- <item>72s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 31s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.07,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 4s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>10s</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 | 0.0852 0.0000 0.0852 | 32.0000</item>
- <item>2 | 2.50 | 0.0825 0.0012 0.0837 | 29.4886</item>
- <item>3 | 2.50 | 0.0817 0.0018 0.0835 | 26.9772</item>
- <item>4 | 2.50 | 0.0813 0.0021 0.0834 | 24.6107</item>
- <item>5 | 2.50 | 0.0810 0.0022 0.0832 | 22.6548</item>
- <item>6 | 2.50 | 0.0807 0.0023 0.0830 | 20.6989</item>
- <item>7 | 2.50 | 0.0804 0.0024 0.0828 | 18.9688</item>
- <item>8 | 2.50 | 0.0801 0.0025 0.0826 | 17.4455</item>
- <item>9 | 2.50 | 0.0798 0.0026 0.0824 | 15.9223</item>
- <item>10 | 2.50 | 0.0795 0.0027 0.0822 | 14.6627</item>
- <item>11 | 2.50 | 0.0792 0.0028 0.0819 | 13.4764</item>
- <item>12 | 2.50 | 0.0788 0.0028 0.0817 | 12.3015</item>
- <item>13 | 2.50 | 0.0785 0.0029 0.0814 | 11.3776</item>
- <item>14 | 2.50 | 0.0782 0.0030 0.0812 | 10.4537</item>
- <item>15 | 2.25 | 0.0778 0.0031 0.0809 | 9.5920</item>
- <item>16 | 2.25 | 0.0748 0.0046 0.0794 | 8.8725</item>
- <item>29 | 2.00 | 0.0761 0.0021 0.0782 | 3.3283</item>
- <item>30 | 2.00 | 0.0698 0.0046 0.0744 | 3.1221</item>
- <item>31 | 2.00 | 0.0677 0.0056 0.0733 | 2.9160</item>
- <item>43 | 1.75 | 0.0665 0.0033 0.0698 | 1.5785</item>
- <item>44 | 1.75 | 0.0622 0.0056 0.0677 | 1.5194</item>
- <item>45 | 1.75 | 0.0607 0.0064 0.0671 | 1.4626</item>
- <item>57 | 1.50 | 0.0592 0.0046 0.0639 | 1.0900</item>
- <item>58 | 1.50 | 0.0561 0.0067 0.0628 | 1.0730</item>
- <item>59 | 1.50 | 0.0550 0.0074 0.0624 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 132s</item>
- <item>Prepare output 10s</item>
- <item>142s</item>
- <item>Jacobian determinant (RMS): 0.011 0.040 0.060 0.084 0.106 | 0.113373</item>
- <item>Template Matching: 0.085 0.225 0.203 0.182 0.165 | 0.165037</item>
- <item>Write result maps: 26s</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: 14s</item>
- <item>PBT2x thickness: 42s</item>
- <item>98s</item>
- <item>Create initial surface 69s</item>
- <item>Topology correction: 83s</item>
- <item>Surface refinement: 76s</item>
- <item>Reduction of surface collisions with optimization: 66s</item>
- <item>Spherical mapping with areal smoothing 71s</item>
- <item>Spherical registration 243s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 42s</item>
- <item>100s</item>
- <item>Create initial surface 69s</item>
- <item>Topology correction: 82s</item>
- <item>Surface refinement: 67s</item>
- <item>Reduction of surface collisions with optimization: 63s</item>
- <item>Spherical mapping with areal smoothing 68s</item>
- <item>Spherical registration 248s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6068 0.6518 mm</item>
- <item>Surface intensity / position RMSE: 0.0650 / 0.0679</item>
- <item>Euler number / defect number / defect size: 18.0 / 11.5 / 0.68%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_26479/ds/sub-002/surf/lh.thickness.sub-002_ses-03_acq-PHILLIPS_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_26479/ds/sub-002/surf/rh.thickness.sub-002_ses-03_acq-PHILLIPS_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_26479/ds/sub-002/sub-002_ses-03_acq-PHILLIPS_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1491s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 33s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 23s</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 21s</item>
- <item>ROI estimation of 'anatomy3' atlas 30s</item>
- <item>ROI estimation of 'julichbrain' atlas 39s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 28s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 63s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 94s</item>
- <item>Write results 94s</item>
- <item>391s</item>
- <item>Quality check: 4s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_26479/ds/sub-002/report/catreport_sub-002_ses-03_acq-PHILLIPS_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 44 minute(s) and 46 second(s).</item>
- <item>Image Quality Rating (IQR): 82.33% (B-)</item>
- <item>GM volume (GMV): 46.29% (767.95 / 1658.96 ml)</item>
- <item>GM thickness (GMT): 2.61 0.65 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_26479/ds/sub-002/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_26479/ds/sub-002/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_26479/ds/sub-002/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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