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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
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- <ngaus>[1 1 2 3 4 2]</ngaus>
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- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
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- <regstr>0.5</regstr>
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- <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>
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- <shootingsurf>Template_T1</shootingsurf>
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- <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>
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- <reduce_mesh>1</reduce_mesh>
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- <thick_limit>5</thick_limit>
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- <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>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
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- <item>csf</item>
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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>
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- <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>
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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>
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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>
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- <item>gm</item>
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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>
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- <item>csf</item>
- <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/aal3.nii</td>
- <td>1</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/mori.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/anatomy3.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/julichbrain.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <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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- <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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- <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>
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- <item>gm</item>
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- <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>/var/lib/condor/execute/dir_3209399/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
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- <item>gm</item>
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- <item>csf</item>
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- <td>[false]</td>
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- <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>
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- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
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- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
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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>
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- <qualitymeasures>
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- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>1.28897255232768</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0795677751302719</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.101201638579369</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>185.879684448242</res_BB>
- <tissue_mn>[4.75 110.212997436523 247.828994750977 360.457000732422]</tissue_mn>
- <tissue_mnr>[0.0131777161732316 0.305759072303772 0.68754106760025 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[2.35437252928888 42.7922194721403 34.4057337888639 23.7510314315079]</tissue_std>
- <tissue_stdr>[0.00661885365843773 0.120301872491837 0.0967249274253845 0.0667713358998299]</tissue_stdr>
- <contrast>114.13200378418</contrast>
- <contrastr>0.316631406545639</contrastr>
- <res_ECR>0.345955789089203</res_ECR>
- <NCR>0.143376380205154</NCR>
- <ICR>0.322246253490448</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.66303968429565</res_ECR>
- <res_BB>10.5</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>3.3338623046875</contrastr>
- <NCR>2.3892674446106</NCR>
- <ICR>1.25904333591461</ICR>
- <SurfaceEulerNumber>2.22448979591837</SurfaceEulerNumber>
- <SurfaceDefectArea>1.32224313808192</SurfaceDefectArea>
- <SurfaceDefectNumber>1.575</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.59135556221008</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.02403259277344</SurfacePositionRMSE>
- <SIQR>2.4462781451878</SIQR>
- <IQR>2.25091986007409</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>
- <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>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>20231031-011804</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>1.28897255232768</SurfaceDefectArea>
- <SurfaceDefectNumber>11.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0795677751302719</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.101201638579369</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>26</EC_abs>
- <defect_size>1.28897255232768</defect_size>
- <vol_abs_CGW>[222.576384313725 760.710078431372 465.29911372549 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.455380392156863</vol_abs_WMH>
- <vol_rel_WMH>0.00031436209192858</vol_rel_WMH>
- <surf_TSA>2000.68405373443</surf_TSA>
- <vol_TIV>1448.58557647059</vol_TIV>
- <vol_rel_CGW>[0.153650835635146 0.525139895624812 0.321209268740042 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.59100845223324 0.673984605561876]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.60293745994568 0.883479992239724 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.91667462968158 0.309833204374247 0.283248463984317;2.62076414393143 0.198262267381674 0.443806928207703;3.35019551711002 0.309971485190043 0.27294460780798]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.748216328516269 0.291118357773141 0.633060007454342;4.38341906471504 0.331008234375525 0.366939992545658]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.05603337405519</vol_TIV>
- <vol_rel_CGW>[0.609390007815121 7.28124812544561 3.61870094719903 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.03143620919286</vol_rel_WMH>
- <surf_TSA>8.621468549777</surf_TSA>
- <SQR>5.95711878846449</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.336 0.410736492443716]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00752045447006822 0.00119860656559467 0.385592222213745]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[873.909082352941 429.491321568627 432.652188235294 880.823898039216 2013.08870196078 7462.80803529412]</SPMvols0>
- <SPMvols1>[758.928556862745 400.424466666667 255.315109803922 757.07857254902 1891.53311372549 7471.717]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[140.976898193359 265.28271484375 347.678314208984]</T3th>
- <Tth>
- <T3th>[-5.84790992736816 26.4997253417969 4.97843265533447 140.976898193359 265.28271484375 347.678314208984 451.029022216797 1116.21545410156]</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>[0.0191809684038162 0.0676828995347023 0.0744331479072571 0 0]</dtc>
- <ll>[0.082084084854645 0 0.082084084854645 0;0.19945078251027 0.00922307017899933 0.208673852689269 1966.80126953125;0.19945078251027 0.00922307017899933 0.208673852689269 1966.80126953125]</ll>
- <rmsdtc>[0.0440570302307606 0.0908507406711578 0.101241670548916]</rmsdtc>
- <rmsgdt>[0.0317341387271881 0.0434123799204826 0.0536123663187027]</rmsgdt>
- <rmsdt>0.101241670548916</rmsdt>
- <dt>0.0744331479072571</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>[0.00858565233647823 0.0302341766655445 0.0425286293029785 0.0518113449215889 0.0594583041965961 0.0665293484926224]</dtc>
- <ll>[0.081359433606449 0 0.081359433606449 0;0.217345741758242 0.0112628710699023 0.228608612828144 5765.18212890625;0.201108980918756 0.0144878073842384 0.215596788302995 10427.048828125;0.182764008061046 0.017328092062462 0.200092100123508 18684.396484375;0.166690252767738 0.0209034291892488 0.187593681956986 36567.4765625;0.166690252767738 0.0209034291892488 0.187593681956986 36567.4765625]</ll>
- <rmsdtc>[0.0102991694584489 0.0363444685935974 0.054956927895546 0.0803405120968819 0.106316104531288 0.113708607852459]</rmsdtc>
- <rmsgdt>[0.00303160259500146 0.0119376545771956 0.0273650698363781 0.0487411171197891 0.0691791847348213 0.0756246671080589]</rmsgdt>
- <rmsdt>0.113708607852459</rmsdt>
- <dt>0.0665293484926224</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025647/ses-1/sub-0025647_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 82s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 8s</item>
- <item>45s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 64s</item>
- <item>SPM preprocessing 1 (estimate 2): 59s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 17s</item>
- <item>Update Segmentation 19s</item>
- <item>Update Skull-Stripping 41s</item>
- <item>Update probability maps 9s</item>
- <item>86s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 24s</item>
- <item>Fast Optimized Shooting registration 33s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.03) 14s</item>
- <item>Estimate local tissue thresholds (WM) 19s</item>
- <item>Estimate local tissue thresholds (GM) 28s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 45s</item>
- <item>115s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 9s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 25s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>71s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 33s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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) 3s</item>
- <item>11s</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 | 0.0814 0.0000 0.0814 | 32.0000</item>
- <item>2 | 2.50 | 0.0794 0.0010 0.0803 | 29.4886</item>
- <item>3 | 2.50 | 0.0788 0.0015 0.0802 | 26.9772</item>
- <item>4 | 2.50 | 0.0785 0.0016 0.0801 | 24.6107</item>
- <item>5 | 2.50 | 0.0782 0.0018 0.0800 | 22.6548</item>
- <item>6 | 2.50 | 0.0780 0.0018 0.0799 | 20.6989</item>
- <item>7 | 2.50 | 0.0778 0.0019 0.0797 | 18.9688</item>
- <item>8 | 2.50 | 0.0776 0.0020 0.0796 | 17.4455</item>
- <item>9 | 2.50 | 0.0774 0.0021 0.0794 | 15.9223</item>
- <item>10 | 2.50 | 0.0771 0.0022 0.0793 | 14.6627</item>
- <item>11 | 2.50 | 0.0769 0.0022 0.0791 | 13.4764</item>
- <item>12 | 2.50 | 0.0766 0.0023 0.0789 | 12.3015</item>
- <item>13 | 2.50 | 0.0763 0.0024 0.0787 | 11.3776</item>
- <item>14 | 2.50 | 0.0761 0.0024 0.0785 | 10.4537</item>
- <item>15 | 2.25 | 0.0748 0.0025 0.0773 | 9.5920</item>
- <item>16 | 2.25 | 0.0724 0.0038 0.0762 | 8.8725</item>
- <item>29 | 2.00 | 0.0743 0.0017 0.0760 | 3.3283</item>
- <item>30 | 2.00 | 0.0688 0.0039 0.0728 | 3.1221</item>
- <item>31 | 2.00 | 0.0670 0.0048 0.0719 | 2.9160</item>
- <item>43 | 1.75 | 0.0665 0.0027 0.0692 | 1.5785</item>
- <item>44 | 1.75 | 0.0623 0.0050 0.0673 | 1.5194</item>
- <item>45 | 1.75 | 0.0609 0.0058 0.0667 | 1.4626</item>
- <item>57 | 1.50 | 0.0599 0.0042 0.0640 | 1.0900</item>
- <item>58 | 1.50 | 0.0566 0.0063 0.0629 | 1.0730</item>
- <item>59 | 1.50 | 0.0556 0.0070 0.0625 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 169s</item>
- <item>Prepare output 10s</item>
- <item>179s</item>
- <item>Jacobian determinant (RMS): 0.010 0.036 0.055 0.080 0.106 | 0.113709</item>
- <item>Template Matching: 0.081 0.217 0.201 0.183 0.167 | 0.166690</item>
- <item>Write result maps: 34s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 32s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 47s</item>
- <item>101s</item>
- <item>Create initial surface 84s</item>
- <item>Topology correction: 95s</item>
- <item>Surface refinement: 92s</item>
- <item>Reduction of surface collisions with optimization: 75s</item>
- <item>Spherical mapping with areal smoothing 84s</item>
- <item>Spherical registration 300s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 46s</item>
- <item>95s</item>
- <item>Create initial surface 85s</item>
- <item>Topology correction: 104s</item>
- <item>Surface refinement: 84s</item>
- <item>Reduction of surface collisions with optimization: 78s</item>
- <item>Spherical mapping with areal smoothing 92s</item>
- <item>Spherical registration 310s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5910 0.6739 mm</item>
- <item>Surface intensity / position RMSE: 0.0796 / 0.1012</item>
- <item>Euler number / defect number / defect size: 26.0 / 11.5 / 1.29%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/surf/lh.thickness.sub-0025647_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/surf/rh.thickness.sub-0025647_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/sub-0025647_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 10s</item>
- <item>Surface and thickness estimation takes: 1780s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 41s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 29s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 16s</item>
- <item>ROI estimation of 'mori' atlas 20s</item>
- <item>ROI estimation of 'anatomy3' atlas 31s</item>
- <item>ROI estimation of 'julichbrain' atlas 40s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 32s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 67s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 100s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 9s</item>
- <item>Write results 10s</item>
- <item>436s</item>
- <item>Quality check: 12s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/report/catreport_sub-0025647_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 53 minute(s) and 34 second(s).</item>
- <item>Image Quality Rating (IQR): 82.49% (B-)</item>
- <item>GM volume (GMV): 52.51% (760.71 / 1448.59 ml)</item>
- <item>GM thickness (GMT): 2.59 0.67 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3209399/ds/SWU_4/sub-0025647/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|