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- <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>
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- <tol>0.0001</tol>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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- <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_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
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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>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>
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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>
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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/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>
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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/mori.nii</td>
- <td>1</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/anatomy3.nii</td>
- <td>1</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/julichbrain.nii</td>
- <td>1</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/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</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/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</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/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</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/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/var/lib/condor/execute/dir_1964201/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
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- <td>[false]</td>
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- <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>
- </tr>
- <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>
- </tr>
- <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>
- </tr>
- <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>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
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- <shootingtpm>
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- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
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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_4_GS.nii</item>
- </shootingtpms>
- <inv_weighting>[true]</inv_weighting>
- <histth>[0.96 0.9999]</histth>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software/>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>1.65202626628963</SurfaceDefectArea>
- <SurfaceDefectNumber>13.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.092839851975441</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.102781176567078</SurfacePositionRMSE>
- <res_vx_vol>[0.699999988079071 0.699999988079071 0.699999988079071]</res_vx_vol>
- <res_vx_voli>[0.700000047683716 0.699999988079071 0.699999988079071]</res_vx_voli>
- <res_RMS>0.699999988079071</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 2269.291015625 1635.81298828125 1156.17102050781]</tissue_mn>
- <tissue_mnr>[0 1.38725578784943 1 0.706786811351776]</tissue_mnr>
- <tissue_weighting>inverse</tissue_weighting>
- <tissue_std>[0 564.09813829439 347.520806617647 73.4587481713832]</tissue_std>
- <tissue_stdr>[0 0.487901985645294 0.300579071044922 0.0635362267494202]</tissue_stdr>
- <contrast>479.641998291016</contrast>
- <contrastr>0.293213218450546</contrastr>
- <res_ECR>1</res_ECR>
- <NCR>0.140314221382141</NCR>
- <ICR>0.134847819805145</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.39999997615814 1.39999997615814 1.39999997615814]</res_vx_vol>
- <res_RMS>1.39999997615814</res_RMS>
- <res_ECR>6</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[1.89584361469504 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.68513488769531</contrastr>
- <NCR>2.34530901908875</NCR>
- <ICR>0.794265389442444</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.41300656657241</SurfaceDefectArea>
- <SurfaceDefectNumber>1.675</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.85679697990417</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.05562353134155</SurfacePositionRMSE>
- <SIQR>5.23047521043469</SIQR>
- <IQR>2.1549617471378</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
- <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>
- <system>LINUX</system>
- <version_spm>7771</version_spm>
- <version_matlab>9.3</version_matlab>
- <version_cat>12.8.1</version_cat>
- <revision_cat>2040</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>20231031-050548</date>
- <cat_warnings>
- <item>
- <identifier>cat_run_job1639:nonT1contrast</identifier>
- <message>A non-T1 contrast was detected and the NEW EXPERIMENTAL </br>PIPELINE is used! If it is was a high-resolution T1 image, </br>the initial segmentation might have failed, probably due </br>to alignment problems (please check the image orientation).</message>
- <level>1</level>
- <data>[3218.95803994859 2080.8091 1322.04313 1791.86714 1750.4892 1861.76774]</data>
- </item>
- <item>
- <identifier>cat_main:skipLAS</identifier>
- <message>Skip LAS due to image contrast. Use global normalization.</message>
- <level>0</level>
- </item>
- </cat_warnings>
- </software>
- <subjectmeasures>
- <software/>
- <qualitymeasures>
- <software/>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>1.65202626628963</SurfaceDefectArea>
- <SurfaceDefectNumber>13.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.092839851975441</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.102781176567078</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>1.65202626628963</defect_size>
- <vol_abs_CGW>[302.454718760369 696.229335580094 415.164988003179 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0</vol_abs_WMH>
- <vol_rel_WMH>0</vol_rel_WMH>
- <surf_TSA>1663.4072930368</surf_TSA>
- <vol_TIV>1413.84904234364</vol_TIV>
- <vol_rel_CGW>[0.213922922251311 0.492435411934786 0.293641665813903 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.61753902038277 0.822901175341398]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.62319898605347 1.24600354066758 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[0.99382354231217 0.510894459608607 0.107707844805523;2.4239754461515 0.325045579077428 0.533302897618405;3.49233253760393 0.513893048506619 0.358989257576072]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[4.65760581970215 0.0858214641123047 0.357327307940607;4.97873735707253 0.047110590722573 0.642672692059393]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.0045681699452</vol_TIV>
- <vol_rel_CGW>[1.69186282778934 6.69388311664487 3.12359313602556 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1</vol_rel_WMH>
- <surf_TSA>8.44429007210899</surf_TSA>
- <SQR>5.47557434706861</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 8429.56756933594 0.192340796223187]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.772643804550171 0.772647857666016 0.00799279473721981]</highBGpara>
- <highBG>[true]</highBG>
- </affreg>
- <SPMvols0>[802.344171931599 424.718434163862 275.68392564464 354.57096911583 2642.42006967871 3927.57347116058]</SPMvols0>
- <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>[0.0162620060145855 0.0580988042056561 0.063623420894146 0 0]</dtc>
- <ll>[0.0858577500824549 0 0.0858577500824549 0;0.221620319270286 0.00895569161349843 0.230576010883785 1909.78332519531;0.221620319270286 0.00895569161349843 0.230576010883785 1909.78332519531]</ll>
- <rmsdtc>[0.0361267291009426 0.080275185406208 0.0937672853469849]</rmsdtc>
- <rmsgdt>[0.0257503781467676 0.046740997582674 0.0602762177586555]</rmsgdt>
- <rmsdt>0.0937672853469849</rmsdt>
- <dt>0.063623420894146</dt>
- </reginitp>
- <SPMvols1>[806.138148864742 425.672668266951 273.775561011014 375.268664554122 2632.11327174335 3916.61440422653]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[3320.75671 2080.8091 1322.04313]</T3th>
- <Tth>
- <T3th>[-1.26684355362816e+15 0 0 0 0 1.21836278742463e+19]</T3th>
- <T3thx>[0 1 1.5 2 3 4]</T3thx>
- </Tth>
- </gintnorm>
- <uintnorm1postlas>
- <Tthm>
- <CGW>[0.688350334663258 0.340578793523753 0.974924679013852]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 1.02173638057126 2.06505100398977 2.92477403704156 4 5 6]</T3thx>
- </Tthm>
- <Tthmi>
- <CGW>[0.688283705290859 0.340588822698858 0.974864774496053]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 1.02176646809657 2.06485111587258 2.92459432348816 4 5 6]</T3thx>
- </Tthmi>
- </uintnorm1postlas>
- <uintnorm2postamap>
- <Tthm>
- <CGW>[0.670606858930897 0.333266895534032 0.997083022166861]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 0.999800686602097 2.01182057679269 2.99124906650058 4 5 6]</T3thx>
- </Tthm>
- <Tthmi>
- <CGW>[0.670616558235644 0.333265089249223 0.997098755315136]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 0.99979526774767 2.01184967470693 2.99129626594541 4 5 6]</T3thx>
- </Tthmi>
- </uintnorm2postamap>
- </tths>
- <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>[0.0132117448374629 0.0510243661701679 0.0743010714650154 0.0853778347373009 0.0930114388465881 0.108112290501595]</dtc>
- <ll>[0.0867437631532001 0 0.0867437631532001 0;0.211382814407814 0.0195603746947497 0.230943189102564 10012.466796875;0.18302496779962 0.020420067169663 0.203445034969283 14696.5673828125;0.163440787667676 0.0201314254137639 0.18357221308144 21707.15234375;0.148405260401989 0.0222676121185947 0.170672872520583 38953.9140625;0.148405260401989 0.0222676121185947 0.170672872520583 38953.9140625]</ll>
- <rmsdtc>[0.0150851933285594 0.0573842935264111 0.087751530110836 0.121727637946606 0.151116043329239 0.159718170762062]</rmsdtc>
- <rmsgdt>[0.00421335455030203 0.0171332098543644 0.0359068140387535 0.0594449527561665 0.0829764679074287 0.0887380987405777]</rmsgdt>
- <rmsdt>0.159718170762062</rmsdt>
- <dt>0.108112290501595</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0027430/ses-1/sub-0027430_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 238s</item>
- <item>Skip initial affine registration due to high-intensity background 13s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 36s</item>
- <item>SPM preprocessing 1 (estimate 2): 87s</item>
- <item>----------------------------------------------------------------------------</item>
- <item>WARNING 01: cat_run_job1639:nonT1contrast</item>
- <item>A non-T1 contrast was detected and the NEW EXPERIMENTAL</item>
- <item>PIPELINE is used! If it is was a high-resolution T1 image,</item>
- <item>the initial segmentation might have failed, probably due</item>
- <item>to alignment problems (please check the image orientation).</item>
- <item>----------------------------------------------------------------------------</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 25s</item>
- <item>Update segmentation 44s</item>
- <item>Update skull-stripping 20s</item>
- <item>Update probability maps 2s</item>
- <item>Update registration 30s</item>
- <item>121s</item>
- <item>Global intensity correction: SANLM denoising after intensity normalization (medium): 82s</item>
- <item>------------------------------------------------------------------------</item>
- <item>NOTE 01: cat_main:skipLAS</item>
- <item>Skip LAS due to image contrast. Use global normalization.</item>
- <item>------------------------------------------------------------------------</item>
- <item>161s</item>
- <item>SANLM denoising after LAS (medium) 83s</item>
- <item>165s</item>
- <item>--- Update Ym and Ymi ---</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 1s</item>
- <item>Ventricle detection 2s</item>
- <item>Blood vessel detection 1s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 0s</item>
- <item>Side alignment 1s</item>
- <item>Final corrections 7s</item>
- <item>18s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 53s</item>
- <item>AMAP peaks: [0.91 0.05,0.64 0.08,0.36 0.04]</item>
- <item>--- Update Ym and Ymi ---</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 | 0.0867 0.0000 0.0867 | 32.0000</item>
- <item>2 | 2.50 | 0.0824 0.0017 0.0841 | 29.4886</item>
- <item>3 | 2.50 | 0.0811 0.0026 0.0837 | 26.9772</item>
- <item>4 | 2.50 | 0.0804 0.0030 0.0834 | 24.6107</item>
- <item>5 | 2.50 | 0.0799 0.0032 0.0831 | 22.6548</item>
- <item>6 | 2.50 | 0.0795 0.0033 0.0828 | 20.6989</item>
- <item>7 | 2.50 | 0.0790 0.0035 0.0825 | 18.9688</item>
- <item>8 | 2.50 | 0.0785 0.0037 0.0822 | 17.4455</item>
- <item>9 | 2.50 | 0.0780 0.0038 0.0818 | 15.9223</item>
- <item>10 | 2.50 | 0.0775 0.0040 0.0814 | 14.6627</item>
- <item>11 | 2.50 | 0.0769 0.0041 0.0810 | 13.4764</item>
- <item>12 | 2.50 | 0.0764 0.0042 0.0806 | 12.3015</item>
- <item>13 | 2.50 | 0.0758 0.0044 0.0802 | 11.3776</item>
- <item>14 | 2.50 | 0.0753 0.0045 0.0798 | 10.4537</item>
- <item>15 | 2.25 | 0.0740 0.0047 0.0787 | 9.5920</item>
- <item>16 | 2.25 | 0.0705 0.0065 0.0770 | 8.8725</item>
- <item>29 | 2.00 | 0.0700 0.0029 0.0729 | 3.3283</item>
- <item>30 | 2.00 | 0.0632 0.0058 0.0690 | 3.1221</item>
- <item>31 | 2.00 | 0.0610 0.0068 0.0678 | 2.9160</item>
- <item>43 | 1.75 | 0.0594 0.0040 0.0634 | 1.5785</item>
- <item>44 | 1.75 | 0.0557 0.0060 0.0617 | 1.5194</item>
- <item>45 | 1.75 | 0.0545 0.0067 0.0612 | 1.4626</item>
- <item>57 | 1.50 | 0.0531 0.0050 0.0581 | 1.0900</item>
- <item>58 | 1.50 | 0.0503 0.0068 0.0572 | 1.0730</item>
- <item>59 | 1.50 | 0.0495 0.0074 0.0569 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 104s</item>
- <item>Prepare output 12s</item>
- <item>116s</item>
- <item>Jacobian determinant (RMS): 0.015 0.057 0.088 0.122 0.151 | 0.159718</item>
- <item>Template Matching: 0.087 0.211 0.183 0.163 0.148 | 0.148405</item>
- <item>Write result maps: 43s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 16s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 26s</item>
- <item>58s</item>
- <item>Create initial surface 47s</item>
- <item>Topology correction: 50s</item>
- <item>Surface refinement: 39s</item>
- <item>Reduction of surface collisions with optimization: 36s</item>
- <item>Spherical mapping with areal smoothing 47s</item>
- <item>Spherical registration 185s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 16s</item>
- <item>CSF distance: 9s</item>
- <item>PBT2x thickness: 27s</item>
- <item>56s</item>
- <item>Create initial surface 47s</item>
- <item>Topology correction: 53s</item>
- <item>Surface refinement: 41s</item>
- <item>Reduction of surface collisions with optimization: 38s</item>
- <item>Spherical mapping with areal smoothing 48s</item>
- <item>Spherical registration 185s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6171 0.8203 mm</item>
- <item>Surface intensity / position RMSE: 0.0928 / 0.1028</item>
- <item>Euler number / defect number / defect size: 18.0 / 13.5 / 1.65%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/surf/lh.thickness.sub-0027430_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/surf/rh.thickness.sub-0027430_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/sub-0027430_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 1559s</item>
- <item>Surface and thickness estimation takes: 1298s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 46s</item>
- <item>ROI estimation of 'lpba40' atlas 13s</item>
- <item>ROI estimation of 'hammers' atlas 33s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 19s</item>
- <item>ROI estimation of 'mori' atlas 27s</item>
- <item>ROI estimation of 'anatomy3' atlas 38s</item>
- <item>ROI estimation of 'julichbrain' atlas 51s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 36s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 122s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 10s</item>
- <item>Write results 11s</item>
- <item>527s</item>
- <item>Quality check: 16s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/report/catreport_sub-0027430_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 44 minute(s) and 31 second(s).</item>
- <item>Image Quality Rating (IQR): 83.45% (B)</item>
- <item>GM volume (GMV): 49.24% (696.23 / 1413.85 ml)</item>
- <item>GM thickness (GMT): 2.62 0.82 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1964201/ds/MPG_1/sub-0027430/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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