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- <F>/var/lib/condor/execute/dir_12014/ds/sub-013/sub-013_ses-t1_T1w.nii</F>
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- <Fp0>/var/lib/condor/execute/dir_12014/ds/sub-013/mri/p0sub-013_ses-t1_T1w.nii</Fp0>
- <fnames>..2014/ds/sub-013/sub-013_ses-t1_T1w</fnames>
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- <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>
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- </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>
- <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>
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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>
- </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>
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- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </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>
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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>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <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>
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- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
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- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
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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>
- <HC>19</HC>
- <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>
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- </shootingtpm>
- <regstr>0.5</regstr>
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- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
- <darteltpms>
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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>
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- <AMAPframing>1</AMAPframing>
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- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.154131345325603</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0575631409883499</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0577083565294743</SurfacePositionRMSE>
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- <res_vx_voli>[1.00001159812408 1.00000000720084 1.00000000156391]</res_vx_voli>
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- <tissue_mn>[0 8236.2880859375 19326.923828125 27634.88671875]</tissue_mn>
- <tissue_mnr>[0 0.298039495944977 0.699366867542267 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[1442.36878123721 3025.55082612789 2770.64017756108 1632.85462834387]</tissue_std>
- <tissue_stdr>[0.0521937645971775 0.109483018517494 0.100258782505989 0.0590867139399052]</tissue_stdr>
- <contrast>8307.962890625</contrast>
- <contrastr>0.300633132457733</contrastr>
- <NCR>0.136924475431442</NCR>
- <ICR>0.269577145576477</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00002319386665 2.00000001447116 2.00000000369865]</res_vx_vol>
- <res_RMS>2.00000773737535</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.57383632659912</contrastr>
- <NCR>2.29664754867554</NCR>
- <ICR>1.12841558456421</ICR>
- <SurfaceEulerNumber>1.40816326530612</SurfaceEulerNumber>
- <SurfaceDefectArea>1.0385328363314</SurfaceDefectArea>
- <SurfaceDefectNumber>1.6</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.15126276016235</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.15416717529297</SurfacePositionRMSE>
- <IQR>2.18261744809548</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>20220713-030843</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.154131345325603</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0575631409883499</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0577083565294743</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>10</EC_abs>
- <defect_size>0.154131345325603</defect_size>
- <vol_abs_CGW>[328.21182516026 642.748903365798 521.438334559529 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.826578221341235</vol_abs_WMH>
- <vol_rel_WMH>0.000553858710975237</vol_rel_WMH>
- <surf_TSA>1915.54147043761</surf_TSA>
- <vol_TIV>1492.39906308559</vol_TIV>
- <vol_rel_CGW>[0.219922293760806 0.430681658320592 0.349396047918602 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.48012816985044 0.657370467244731]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.46887278556824 0.825242921044891 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.77600798712639 0.288112119521701 0.268483549160035;2.47306183608212 0.195577002086574 0.458028288674574;3.19345059522613 0.305072550703466 0.273488162165391]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.781244608043076 0.224266768306754 0.497291102312982;4.27494370742165 0.376334744391814 0.502708897687018]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.20071851983431</vol_TIV>
- <vol_rel_CGW>[1.79961016093401 5.58479989799914 4.12492902152662 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05538587109752</vol_rel_WMH>
- <surf_TSA>8.61536538804119</surf_TSA>
- <SQR>4.61582195716647</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.601162037037037 1338 549 4135.19999264994 0.364175123243889]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.350841104984283]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[785.435430081479 471.079118679938 506.944060445698 798.418749403126 2794.65182507214 5809.55663793913]</SPMvols0>
- <SPMvols1>[685.675476113781 440.738652800118 323.012227554906 1707.04193086318 2253.99148701539 4957.68429556427]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[9774.908203125 20598.5625 26894.921875]</T3th>
- <Tth>
- <T3th>[0 0 252.438873291016 9774.908203125 20598.5625 26894.921875 35454.9296875 48698.5234375]</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>[0.0198993403464556 0.0767510831356049 0.0850138962268829 0 0]</dtc>
- <ll>[0.0870150428335397 0 0.0870150428335397 0;0.201823368507559 0.0115384769325211 0.21336184544008 2460.55712890625;0.201823368507559 0.0115384769325211 0.21336184544008 2460.55712890625]</ll>
- <rmsdtc>[0.0441877655684948 0.101931408047676 0.113469541072845]</rmsdtc>
- <rmsgdt>[0.0317305214703083 0.046573493629694 0.0578092262148857]</rmsgdt>
- <rmsdt>0.113469541072845</rmsdt>
- <dt>0.0850138962268829</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>[0.00973933283239603 0.0409109145402908 0.0530307702720165 0.0614206977188587 0.0677149146795273 0.0763858780264854]</dtc>
- <ll>[0.087539555815752 0 0.087539555815752 0;0.222173977411477 0.0180706215659341 0.240244598977411 9249.8994140625;0.203192018995098 0.0190501982042817 0.22224221719938 13710.65625;0.181610918905434 0.0203980991983006 0.202009018103735 21994.69921875;0.163858027082013 0.0230420680888877 0.1869000951709 40308.7109375;0.163858027082013 0.0230420680888877 0.1869000951709 40308.7109375]</ll>
- <rmsdtc>[0.0115463715046644 0.0432760193943977 0.067118227481842 0.0913735553622246 0.115400940179825 0.121753565967083]</rmsdtc>
- <rmsgdt>[0.00332170259207487 0.0132584804669023 0.0291080661118031 0.0490185134112835 0.0699762776494026 0.0725371763110161]</rmsgdt>
- <rmsdt>0.121753565967083</rmsdt>
- <dt>0.0763858780264854</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_12014/ds/sub-013/sub-013_ses-t1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 11s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 6s</item>
- <item>36s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 65s</item>
- <item>SPM preprocessing 1 (estimate 2): 52s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 13s</item>
- <item>Update Segmentation 16s</item>
- <item>Update Skull-Stripping 34s</item>
- <item>Update probability maps 7s</item>
- <item>69s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 5s</item>
- <item>Fast Optimized Shooting registration 27s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.05) 12s</item>
- <item>Estimate local tissue thresholds (WM) 14s</item>
- <item>Estimate local tissue thresholds (GM) 18s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 12s</item>
- <item>64s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 11s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.14) 22s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 3s</item>
- <item>58s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 29s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 4s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>9s</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 | 0.0875 0.0000 0.0875 | 32.0000</item>
- <item>2 | 2.50 | 0.0846 0.0013 0.0859 | 29.4886</item>
- <item>3 | 2.50 | 0.0837 0.0020 0.0856 | 26.9772</item>
- <item>4 | 2.50 | 0.0832 0.0022 0.0854 | 24.6107</item>
- <item>5 | 2.50 | 0.0828 0.0024 0.0853 | 22.6548</item>
- <item>6 | 2.50 | 0.0825 0.0025 0.0850 | 20.6989</item>
- <item>7 | 2.50 | 0.0822 0.0027 0.0848 | 18.9688</item>
- <item>8 | 2.50 | 0.0818 0.0028 0.0846 | 17.4455</item>
- <item>9 | 2.50 | 0.0815 0.0029 0.0844 | 15.9223</item>
- <item>10 | 2.50 | 0.0811 0.0030 0.0841 | 14.6627</item>
- <item>11 | 2.50 | 0.0808 0.0031 0.0839 | 13.4764</item>
- <item>12 | 2.50 | 0.0804 0.0032 0.0836 | 12.3015</item>
- <item>13 | 2.50 | 0.0800 0.0033 0.0833 | 11.3776</item>
- <item>14 | 2.50 | 0.0796 0.0034 0.0830 | 10.4537</item>
- <item>15 | 2.25 | 0.0798 0.0035 0.0833 | 9.5920</item>
- <item>16 | 2.25 | 0.0765 0.0051 0.0816 | 8.8725</item>
- <item>17 | 2.25 | 0.0750 0.0057 0.0807 | 8.1530</item>
- <item>18 | 2.25 | 0.0741 0.0060 0.0801 | 7.5234</item>
- <item>29 | 2.00 | 0.0755 0.0029 0.0784 | 3.3283</item>
- <item>30 | 2.00 | 0.0697 0.0054 0.0751 | 3.1221</item>
- <item>31 | 2.00 | 0.0677 0.0064 0.0741 | 2.9160</item>
- <item>43 | 1.75 | 0.0665 0.0036 0.0701 | 1.5785</item>
- <item>44 | 1.75 | 0.0620 0.0060 0.0680 | 1.5194</item>
- <item>45 | 1.75 | 0.0605 0.0068 0.0673 | 1.4626</item>
- <item>57 | 1.50 | 0.0588 0.0050 0.0638 | 1.0900</item>
- <item>58 | 1.50 | 0.0557 0.0071 0.0627 | 1.0730</item>
- <item>59 | 1.50 | 0.0546 0.0077 0.0623 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 142s</item>
- <item>Prepare output 8s</item>
- <item>150s</item>
- <item>Jacobian determinant (RMS): 0.012 0.043 0.067 0.091 0.115 | 0.121754</item>
- <item>Template Matching: 0.088 0.222 0.203 0.182 0.164 | 0.163858</item>
- <item>Write result maps: 19s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 37s</item>
- <item>94s</item>
- <item>Create initial surface 73s</item>
- <item>Topology correction: 78s</item>
- <item>Surface refinement: 67s</item>
- <item>Reduction of surface collisions with optimization: 55s</item>
- <item>Spherical mapping with areal smoothing 64s</item>
- <item>Spherical registration 238s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 35s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 36s</item>
- <item>88s</item>
- <item>Create initial surface 67s</item>
- <item>Topology correction: 76s</item>
- <item>Surface refinement: 66s</item>
- <item>Reduction of surface collisions with optimization: 54s</item>
- <item>Spherical mapping with areal smoothing 63s</item>
- <item>Spherical registration 243s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4802 0.6573 mm</item>
- <item>Surface intensity / position RMSE: 0.0576 / 0.0577</item>
- <item>Euler number / defect number / defect size: 10.0 / 12.0 / 0.15%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_12014/ds/sub-013/surf/lh.thickness.sub-013_ses-t1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_12014/ds/sub-013/surf/rh.thickness.sub-013_ses-t1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_12014/ds/sub-013/sub-013_ses-t1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1397s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 6s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 21s</item>
- <item>ROI estimation of 'lpba40' atlas 6s</item>
- <item>ROI estimation of 'hammers' atlas 15s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 5s</item>
- <item>ROI estimation of 'aal3' atlas 9s</item>
- <item>ROI estimation of 'mori' atlas 14s</item>
- <item>ROI estimation of 'anatomy3' atlas 20s</item>
- <item>ROI estimation of 'julichbrain' atlas 26s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 19s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 42s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 63s</item>
- <item>Write results 63s</item>
- <item>260s</item>
- <item>Quality check: 4s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_12014/ds/sub-013/report/catreport_sub-013_ses-t1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 39 minute(s) and 7 second(s).</item>
- <item>Image Quality Rating (IQR): 83.17% (B-)</item>
- <item>GM volume (GMV): 43.07% (642.75 / 1492.40 ml)</item>
- <item>GM thickness (GMT): 2.48 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_12014/ds/sub-013/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_12014/ds/sub-013/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_12014/ds/sub-013/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|