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- <filedata>
- <path>/var/lib/condor/execute/dir_9449/ds/sub-season216</path>
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- <Fm>/var/lib/condor/execute/dir_9449/ds/sub-season216/mri/msub-season216_ses-2_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_9449/ds/sub-season216/mri/p0sub-season216_ses-2_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season216/..son216_ses-2_acq-MPrageHiRes_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
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- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
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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>
- <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/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>
- </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>
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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>[false]</td>
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- </atlas>
- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
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- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
- </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>
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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>
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- <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>
- <LE>27</LE>
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- <new_release>0</new_release>
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- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <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_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
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- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>6</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0421848936437855</SurfaceDefectArea>
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- <res_RMS>0.876669453895673</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[12.1890001296997 316.875610351562 807.093811035156 1152.677734375]</tissue_mn>
- <tissue_mnr>[0.0105745084583759 0.274903893470764 0.700190365314484 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[14.1341309630335 125.639649159908 107.821890194911 58.7517242991167]</tissue_std>
- <tissue_stdr>[0.0123930471017957 0.110162988305092 0.094540074467659 0.0515145137906075]</tissue_stdr>
- <contrast>349.277374267578</contrast>
- <contrastr>0.303013890981674</contrastr>
- <NCR>0.100966066122055</NCR>
- <ICR>0.268094331026077</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.75999779720038 1.74999996437642 1.74999995864491]</res_vx_vol>
- <res_RMS>1.75333890779135</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.53812503814697</contrastr>
- <NCR>1.78044891357422</NCR>
- <ICR>1.12473797798157</ICR>
- <SurfaceEulerNumber>1.20408163265306</SurfaceEulerNumber>
- <SurfaceDefectArea>1.01054622341095</SurfaceDefectArea>
- <SurfaceDefectNumber>1.35</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.19847941398621</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.19495117664337</SurfacePositionRMSE>
- <IQR>1.76725766465844</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>20220712-165132</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>6</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0421848936437855</SurfaceDefectArea>
- <SurfaceDefectNumber>7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0599239692091942</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0597475580871105</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>6</EC_abs>
- <defect_size>0.0421848936437855</defect_size>
- <vol_abs_CGW>[248.729302601664 649.124398174434 527.089539653212 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.72555118866361</vol_abs_WMH>
- <vol_rel_WMH>0.000509179010137284</vol_rel_WMH>
- <surf_TSA>1717.82064365059</surf_TSA>
- <vol_TIV>1424.94324042931</vol_TIV>
- <vol_rel_CGW>[0.174553831720852 0.455544038356829 0.369902129922318 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.64930850840129 0.630204654853114]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.6626877784729 0.801120114677487 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.03586057431757 0.263222800487539 0.284234777679259;2.67228189595693 0.17953777077277 0.42552000813989;3.33001951612109 0.276107979853014 0.290245214180851]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.858745347315299 0.376864404925733 0.598047192839707;4.26070206492122 0.304728795676817 0.401952807160293]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.01480868623683</vol_TIV>
- <vol_rel_CGW>[0.984803012227948 6.0313225279603 4.49321354027152 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05091790101373</vol_rel_WMH>
- <surf_TSA>8.52332654307131</surf_TSA>
- <SQR>4.9884077062431</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.0292434692382812 1 10774 9601.44250056189 0.362697921863408]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00795799307525158 0.00436884444206953 0.224868088960648]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[775.690137676308 470.225115871987 378.058790091262 685.980198173157 1934.0620624622 6096.91505910689]</SPMvols0>
- <SPMvols1>[692.017867557123 448.202838253766 231.780374414157 543.935841316643 1708.61978613152 6266.19219191332]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[362.018188476562 841.227416992188 1132.84313964844]</T3th>
- <Tth>
- <T3th>[0 0 34.9690322875977 362.018188476562 841.227416992188 1132.84313964844 1518.25561523438 2960.33056640625]</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>[0.0215456392616034 0.0788116082549095 0.0872401371598244 0 0]</dtc>
- <ll>[0.0826122563283126 0 0.0826122563283126 0;0.189449314882203 0.010969182594913 0.200418497477116 2339.15625;0.189449314882203 0.010969182594913 0.200418497477116 2339.15625]</ll>
- <rmsdtc>[0.0435803532600403 0.102779760956764 0.1142772808671]</rmsdtc>
- <rmsgdt>[0.0305487159639597 0.0462286174297333 0.0572376400232315]</rmsgdt>
- <rmsdt>0.1142772808671</rmsdt>
- <dt>0.0872401371598244</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>[0.0101980296894908 0.0382095240056515 0.0549959279596806 0.0631656348705292 0.0689137652516365 0.0785843729972839]</dtc>
- <ll>[0.083323358068594 0 0.083323358068594 0;0.215766025641026 0.0141384319673382 0.229904457608364 7237.10986328125;0.190381382587757 0.0175901944436629 0.20797157703142 12659.8740234375;0.168862468723105 0.0190974776221816 0.187959946345287 20592.275390625;0.151657105512724 0.0213734980697149 0.173030603582439 37389.79296875;0.151657105512724 0.0213734980697149 0.173030603582439 37389.79296875]</ll>
- <rmsdtc>[0.0117973797023296 0.0439961068332195 0.0668508484959602 0.0943412035703659 0.118865385651588 0.127053171396255]</rmsdtc>
- <rmsgdt>[0.00344674265943468 0.0139018511399627 0.0299397613853216 0.0507901385426521 0.0686299577355385 0.0744334980845451]</rmsgdt>
- <rmsdt>0.127053171396255</rmsdt>
- <dt>0.0785843729972839</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season216_ses-2_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 56s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 8s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 12s</item>
- <item>Refine background 4s</item>
- <item>Final correction 10s</item>
- <item>Final scaling 9s</item>
- <item>62s</item>
- <item>Correct center-of-mass 8s</item>
- <item>Affine registration 19s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 100s</item>
- <item>SPM preprocessing 1 (estimate 2): 71s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 20s</item>
- <item>Update Segmentation 27s</item>
- <item>Update Skull-Stripping 55s</item>
- <item>Update probability maps 11s</item>
- <item>112s</item>
- <item>Global intensity correction: 20s</item>
- <item>SANLM denoising after intensity normalization (medium): 31s</item>
- <item>Fast Optimized Shooting registration 37s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 7s</item>
- <item>Prepare segments (LASmod = 1.00) 21s</item>
- <item>Estimate local tissue thresholds (WM) 23s</item>
- <item>Estimate local tissue thresholds (GM) 32s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 51s</item>
- <item>144s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 10s</item>
- <item>Major structures 5s</item>
- <item>Ventricle detection 20s</item>
- <item>Blood vessel detection 14s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.05) 41s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 5s</item>
- <item>Final corrections 6s</item>
- <item>103s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 46s</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) 6s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>16s</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 | 0.0833 0.0000 0.0833 | 32.0000</item>
- <item>2 | 2.50 | 0.0807 0.0012 0.0819 | 29.4886</item>
- <item>3 | 2.50 | 0.0799 0.0018 0.0817 | 26.9772</item>
- <item>4 | 2.50 | 0.0795 0.0020 0.0816 | 24.6107</item>
- <item>5 | 2.50 | 0.0792 0.0022 0.0814 | 22.6548</item>
- <item>6 | 2.50 | 0.0789 0.0023 0.0812 | 20.6989</item>
- <item>7 | 2.50 | 0.0786 0.0024 0.0810 | 18.9688</item>
- <item>8 | 2.50 | 0.0783 0.0025 0.0808 | 17.4455</item>
- <item>9 | 2.50 | 0.0780 0.0026 0.0806 | 15.9223</item>
- <item>10 | 2.50 | 0.0777 0.0027 0.0804 | 14.6627</item>
- <item>11 | 2.50 | 0.0773 0.0028 0.0802 | 13.4764</item>
- <item>12 | 2.50 | 0.0770 0.0029 0.0799 | 12.3015</item>
- <item>13 | 2.50 | 0.0766 0.0030 0.0796 | 11.3776</item>
- <item>14 | 2.50 | 0.0763 0.0031 0.0794 | 10.4537</item>
- <item>15 | 2.25 | 0.0751 0.0032 0.0783 | 9.5920</item>
- <item>16 | 2.25 | 0.0719 0.0047 0.0766 | 8.8725</item>
- <item>29 | 2.00 | 0.0723 0.0021 0.0745 | 3.3283</item>
- <item>30 | 2.00 | 0.0657 0.0048 0.0705 | 3.1221</item>
- <item>31 | 2.00 | 0.0635 0.0059 0.0693 | 2.9160</item>
- <item>43 | 1.75 | 0.0619 0.0034 0.0653 | 1.5785</item>
- <item>44 | 1.75 | 0.0577 0.0056 0.0633 | 1.5194</item>
- <item>45 | 1.75 | 0.0563 0.0064 0.0627 | 1.4626</item>
- <item>57 | 1.50 | 0.0543 0.0047 0.0590 | 1.0900</item>
- <item>58 | 1.50 | 0.0515 0.0065 0.0580 | 1.0730</item>
- <item>59 | 1.50 | 0.0506 0.0071 0.0577 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 171s</item>
- <item>Prepare output 12s</item>
- <item>183s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.067 0.094 0.119 | 0.127053</item>
- <item>Template Matching: 0.083 0.216 0.190 0.169 0.152 | 0.151657</item>
- <item>Write result maps: 31s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 31s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 39s</item>
- <item>90s</item>
- <item>Create initial surface 74s</item>
- <item>Topology correction: 70s</item>
- <item>Surface refinement: 67s</item>
- <item>Reduction of surface collisions with optimization: 55s</item>
- <item>Spherical mapping with areal smoothing 74s</item>
- <item>Spherical registration 293s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 39s</item>
- <item>95s</item>
- <item>Create initial surface 74s</item>
- <item>Topology correction: 68s</item>
- <item>Surface refinement: 69s</item>
- <item>Reduction of surface collisions with optimization: 54s</item>
- <item>Spherical mapping with areal smoothing 68s</item>
- <item>Spherical registration 265s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6493 0.6298 mm</item>
- <item>Surface intensity / position RMSE: 0.0599 / 0.0597</item>
- <item>Euler number / defect number / defect size: 6.0 / 7.0 / 0.04%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_9449/ds/sub-season216/surf/lh.thickness.sub-season216_ses-2_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_9449/ds/sub-season216/surf/rh.thickness.sub-season216_ses-2_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_9449/ds/sub-season216/sub-season216_ses-2_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1510s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 35s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 25s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 14s</item>
- <item>ROI estimation of 'mori' atlas 21s</item>
- <item>ROI estimation of 'anatomy3' atlas 29s</item>
- <item>ROI estimation of 'julichbrain' atlas 39s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s</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 93s</item>
- <item>Write results 93s</item>
- <item>393s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_9449/ds/sub-season216/report/catreport_sub-season216_ses-2_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 51 minute(s) and 22 second(s).</item>
- <item>Image Quality Rating (IQR): 87.33% (B+)</item>
- <item>GM volume (GMV): 45.55% (649.12 / 1424.94 ml)</item>
- <item>GM thickness (GMT): 2.65 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_9449/ds/sub-season216/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|