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- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_17534/ds/sub-f8570ui</path>
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- <F>/var/lib/condor/execute/dir_17534/ds/sub-f8570ui/sub-f8570ui_ses-wave1bas_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_17534/ds/sub-f8570ui/mri/msub-f8570ui_ses-wave1bas_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_17534/ds/sub-f8570ui/mri/p0sub-f8570ui_ses-wave1bas_T1w.nii</Fp0>
- <fnames>../ds/sub-f8570ui/sub-f8570ui_ses-wave1bas_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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- <accstr>0.5</accstr>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
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- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
- </opts>
- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>24</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <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>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
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- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
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- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <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>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- </atlas>
- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
- </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>
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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>
- </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>
- <LE>27</LE>
- </LAB>
- <new_release>0</new_release>
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- <regmethod>
- <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>
- </shooting>
- </regmethod>
- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
- <darteltpms>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
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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>
- <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_4_GS.nii</item>
- </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>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.789918191877798</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0669280737638474</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0698816180229187</SurfacePositionRMSE>
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- <res_RMS>0.800000003653389</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[17.923999786377 275.430816650391 779.051452636719 1000.17626953125]</tissue_mn>
- <tissue_mnr>[0.0179208405315876 0.275382280349731 0.778914153575897 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[22.3128335433324 123.767678934532 108.177845399444 65.4086366491307]</tissue_std>
- <tissue_stdr>[0.0227159913629293 0.126003965735435 0.110132448375225 0.0665904656052589]</tissue_stdr>
- <contrast>225.159866333008</contrast>
- <contrastr>0.225120186805725</contrastr>
- <NCR>0.109689496457577</NCR>
- <ICR>1.16106307506561</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.60000005744632 1.59999996508722 1.59999999938679]</res_vx_vol>
- <res_RMS>1.60000000730678</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>4.70653057098389</contrastr>
- <NCR>1.90567755699158</NCR>
- <ICR>3.33944201469421</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.19747954796945</SurfaceDefectArea>
- <SurfaceDefectNumber>1.525</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.33856153488159</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.39763236045837</SurfacePositionRMSE>
- <IQR>1.79639028650185</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>20220711-110538</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.789918191877798</SurfaceDefectArea>
- <SurfaceDefectNumber>10.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0669280737638474</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0698816180229187</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.789918191877798</defect_size>
- <vol_abs_CGW>[247.708754694003 664.491009732134 522.47952285564 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.46599858283267</vol_abs_WMH>
- <vol_rel_WMH>0.00102183017196145</vol_rel_WMH>
- <surf_TSA>1882.98540734898</surf_TSA>
- <vol_TIV>1434.67928728178</vol_TIV>
- <vol_rel_CGW>[0.1726579291204 0.46316345096967 0.36417861990993 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.53457751471159 0.631357695935167]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.54503321647644 0.820465666537441 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.89958997150332 0.277390735596368 0.265610949484263;2.55011184372806 0.180981895380514 0.453696112139646;3.21836021663389 0.29091330238384 0.280692938376091]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.750880786342698 0.319269117112155 0.593839835728953;4.22257100131562 0.342821308828078 0.406160164271047]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.02859943077573</vol_TIV>
- <vol_rel_CGW>[0.950753037363501 6.16816542689781 4.39042061619846 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.10218301719615</vol_rel_WMH>
- <surf_TSA>8.61056315523693</surf_TSA>
- <SQR>5.08450505615903</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.117632762419872 1 1 9020.98393158934 0.451350056259785]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.022904209792614 0.0205978378653526 0.332596242427826]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[783.024589620173 489.482652247576 359.615044613659 1000.72905151599 2091.58996219727 6143.51555805491]</SPMvols0>
- <SPMvols1>[693.681210468842 462.005145752974 233.973033289892 1181.90634451375 1944.64803369618 5707.43510910628]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[353.182006835938 814.594482421875 1086.18762207031]</T3th>
- <Tth>
- <T3th>[0 0 22.803316116333 353.182006835938 814.594482421875 1086.18762207031 1452.6904296875 3091.07739257812]</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>[0.0239502191543579 0.0908129662275314 0.101196117699146 0 0]</dtc>
- <ll>[0.0862915783989377 0 0.0862915783989377 0;0.187585416246577 0.0128513040805922 0.200436720327169 2740.51489257812;0.187585416246577 0.0128513040805922 0.200436720327169 2740.51489257812]</ll>
- <rmsdtc>[0.0529072768986225 0.116897754371166 0.128840550780296]</rmsdtc>
- <rmsgdt>[0.0378593951463699 0.0475662276148796 0.0582091175019741]</rmsgdt>
- <rmsdt>0.128840550780296</rmsdt>
- <dt>0.101196117699146</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>[0.0121755069121718 0.0468684583902359 0.0672685727477074 0.0764876082539558 0.0825799331068993 0.0948947891592979]</dtc>
- <ll>[0.0869861620863647 0 0.0869861620863647 0;0.218998901098901 0.0186855349511599 0.237684436050061 9564.658203125;0.190774334907574 0.0210666867658522 0.211841021673426 15161.947265625;0.167804033328325 0.0218921201294757 0.189696153457801 23605.66015625;0.150178719646635 0.0242768772940624 0.174455596940698 42468.828125;0.150178719646635 0.0242768772940624 0.174455596940698 42468.828125]</ll>
- <rmsdtc>[0.0141757046803832 0.0534848757088184 0.0800337940454483 0.110485523939133 0.141509488224983 0.144964545965195]</rmsdtc>
- <rmsgdt>[0.00377836497500539 0.0149166192859411 0.032097402960062 0.0543416328728199 0.0928320214152336 0.0805669650435448]</rmsgdt>
- <rmsdt>0.144964545965195</rmsdt>
- <dt>0.0948947891592979</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./ds/sub-f8570ui/sub-f8570ui_ses-wave1bas_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 166s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 16s</item>
- <item>Estimate background 15s</item>
- <item>Initial correction 15s</item>
- <item>Refine background 8s</item>
- <item>Final correction 14s</item>
- <item>Final scaling 16s</item>
- <item>98s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 20s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 168s</item>
- <item>SPM preprocessing 1 (estimate 2): 90s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 40s</item>
- <item>Update Segmentation 46s</item>
- <item>Update Skull-Stripping 99s</item>
- <item>Update probability maps 20s</item>
- <item>205s</item>
- <item>Global intensity correction: 40s</item>
- <item>SANLM denoising after intensity normalization (medium): 37s</item>
- <item>Fast Optimized Shooting registration 61s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 11s</item>
- <item>Prepare partitions 5s</item>
- <item>Prepare segments (LASmod = 1.00) 36s</item>
- <item>Estimate local tissue thresholds (WM) 41s</item>
- <item>Estimate local tissue thresholds (GM) 54s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 67s</item>
- <item>222s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 20s</item>
- <item>Major structures 9s</item>
- <item>Ventricle detection 29s</item>
- <item>Blood vessel detection 24s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 68s</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>176s</item>
- <item>Blood vessel correction (BVCstr=0.50): 4s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 83s</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) 11s</item>
- <item>Level 1 cleanup (brain masking) 6s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 7s</item>
- <item>28s</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 | 0.0870 0.0000 0.0870 | 32.0000</item>
- <item>2 | 2.50 | 0.0830 0.0016 0.0846 | 29.4886</item>
- <item>3 | 2.50 | 0.0818 0.0025 0.0842 | 26.9772</item>
- <item>4 | 2.50 | 0.0812 0.0028 0.0840 | 24.6107</item>
- <item>5 | 2.50 | 0.0807 0.0030 0.0837 | 22.6548</item>
- <item>6 | 2.50 | 0.0803 0.0031 0.0834 | 20.6989</item>
- <item>7 | 2.50 | 0.0799 0.0033 0.0832 | 18.9688</item>
- <item>8 | 2.50 | 0.0794 0.0034 0.0829 | 17.4455</item>
- <item>9 | 2.50 | 0.0790 0.0035 0.0825 | 15.9223</item>
- <item>10 | 2.50 | 0.0785 0.0037 0.0822 | 14.6627</item>
- <item>11 | 2.50 | 0.0780 0.0038 0.0819 | 13.4764</item>
- <item>12 | 2.50 | 0.0775 0.0039 0.0815 | 12.3015</item>
- <item>13 | 2.50 | 0.0770 0.0041 0.0811 | 11.3776</item>
- <item>14 | 2.50 | 0.0765 0.0042 0.0807 | 10.4537</item>
- <item>15 | 2.25 | 0.0769 0.0043 0.0812 | 9.5920</item>
- <item>16 | 2.25 | 0.0730 0.0062 0.0792 | 8.8725</item>
- <item>29 | 2.00 | 0.0737 0.0028 0.0765 | 3.3283</item>
- <item>30 | 2.00 | 0.0662 0.0058 0.0720 | 3.1221</item>
- <item>31 | 2.00 | 0.0636 0.0070 0.0706 | 2.9160</item>
- <item>43 | 1.75 | 0.0620 0.0041 0.0662 | 1.5785</item>
- <item>44 | 1.75 | 0.0575 0.0065 0.0640 | 1.5194</item>
- <item>45 | 1.75 | 0.0559 0.0073 0.0632 | 1.4626</item>
- <item>57 | 1.50 | 0.0543 0.0054 0.0597 | 1.0900</item>
- <item>58 | 1.50 | 0.0511 0.0075 0.0586 | 1.0730</item>
- <item>59 | 1.50 | 0.0501 0.0081 0.0582 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 260s</item>
- <item>Prepare output 19s</item>
- <item>278s</item>
- <item>Jacobian determinant (RMS): 0.014 0.053 0.080 0.110 0.142 | 0.144965</item>
- <item>Template Matching: 0.087 0.219 0.191 0.168 0.150 | 0.150179</item>
- <item>Write result maps: 58s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 57s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 61s</item>
- <item>147s</item>
- <item>Create initial surface 109s</item>
- <item>Topology correction: 124s</item>
- <item>Surface refinement: 113s</item>
- <item>Reduction of surface collisions with optimization: 93s</item>
- <item>Spherical mapping with areal smoothing 110s</item>
- <item>Spherical registration 301s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 73s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 60s</item>
- <item>161s</item>
- <item>Create initial surface 106s</item>
- <item>Topology correction: 119s</item>
- <item>Surface refinement: 99s</item>
- <item>Reduction of surface collisions with optimization: 93s</item>
- <item>Spherical mapping with areal smoothing 109s</item>
- <item>Spherical registration 292s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5345 0.6311 mm</item>
- <item>Surface intensity / position RMSE: 0.0669 / 0.0699</item>
- <item>Euler number / defect number / defect size: 12.0 / 10.5 / 0.79%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_17534/ds/sub-f8570ui/surf/lh.thickness.sub-f8570ui_ses-wave1bas_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_17534/ds/sub-f8570ui/surf/rh.thickness.sub-f8570ui_ses-wave1bas_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_17534/ds/sub-f8570ui/sub-f8570ui_ses-wave1bas_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2123s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 28s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 102s</item>
- <item>ROI estimation of 'lpba40' atlas 29s</item>
- <item>ROI estimation of 'hammers' atlas 71s</item>
- <item>ROI estimation of 'thalamus' atlas 5s</item>
- <item>ROI estimation of 'ibsr' atlas 25s</item>
- <item>ROI estimation of 'aal3' atlas 42s</item>
- <item>ROI estimation of 'mori' atlas 62s</item>
- <item>ROI estimation of 'anatomy3' atlas 89s</item>
- <item>ROI estimation of 'julichbrain' atlas 120s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 44s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 58s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 193s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 298s</item>
- <item>Write results 300s</item>
- <item>1170s</item>
- <item>Quality check: 10s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_17534/ds/sub-f8570ui/report/catreport_sub-f8570ui_ses-wave1bas_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 87 minute(s) and 30 second(s).</item>
- <item>Image Quality Rating (IQR): 87.04% (B+)</item>
- <item>GM volume (GMV): 46.32% (664.49 / 1434.68 ml)</item>
- <item>GM thickness (GMT): 2.53 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_17534/ds/sub-f8570ui/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_17534/ds/sub-f8570ui/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_17534/ds/sub-f8570ui/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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