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- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_4103490/ds/sub-f6950qp</path>
- <file>sub-f6950qp_ses-wave1bas_T1w</file>
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- <F>/var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/sub-f6950qp_ses-wave1bas_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/mri/msub-f6950qp_ses-wave1bas_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/mri/p0sub-f6950qp_ses-wave1bas_T1w.nii</Fp0>
- <fnames>../ds/sub-f6950qp/sub-f6950qp_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>
- <tol>0.0001</tol>
- <accstr>0.5</accstr>
- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
- <redspmres>0</redspmres>
- <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>20</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>
- <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/lpba40.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/cobra.nii</td>
- <td>0</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/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <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/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>
- </tr>
- <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>
- </tr>
- <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>
- </tr>
- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
- <new_release>0</new_release>
- <lazy>0</lazy>
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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>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_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>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <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>
- </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>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <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>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.397382834515135</SurfaceDefectArea>
- <SurfaceDefectNumber>4.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0704527199268341</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0719440877437592</SurfacePositionRMSE>
- <res_vx_vol>[0.800000732706648 0.799999975698412 0.800000008156315]</res_vx_vol>
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- <res_RMS>0.800000238853868</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[21.1940002441406 245.141372680664 702.766906738281 906.974975585938]</tissue_mn>
- <tissue_mnr>[0.02336779050529 0.270284593105316 0.774847090244293 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[22.2004894741946 124.673443027249 97.4977367348431 57.7346719874963]</tissue_std>
- <tissue_stdr>[0.0250631831586361 0.140749752521515 0.110069803893566 0.0651794001460075]</tissue_stdr>
- <contrast>209.094116210938</contrast>
- <contrastr>0.230540126562119</contrastr>
- <NCR>0.113259270787239</NCR>
- <ICR>0.986108303070068</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.6000014654133 1.59999995139682 1.60000001631263]</res_vx_vol>
- <res_RMS>1.60000047770774</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>4.62523126602173</contrastr>
- <NCR>1.95692324638367</NCR>
- <ICR>2.90552663803101</ICR>
- <SurfaceEulerNumber>1.61224489795918</SurfaceEulerNumber>
- <SurfaceDefectArea>1.09934570862878</SurfaceDefectArea>
- <SurfaceDefectNumber>1.225</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.40905439853668</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.43888175487518</SurfacePositionRMSE>
- <IQR>1.83581523239807</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>20220709-232204</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>14</SurfaceEulerNumber>
- <SurfaceDefectArea>0.397382834515135</SurfaceDefectArea>
- <SurfaceDefectNumber>4.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0704527199268341</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0719440877437592</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>14</EC_abs>
- <defect_size>0.397382834515135</defect_size>
- <vol_abs_CGW>[213.81505555739 681.500779597351 507.189647436397 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.13235025202936</vol_abs_WMH>
- <vol_rel_WMH>0.000807376702683069</vol_rel_WMH>
- <surf_TSA>1854.23078915</surf_TSA>
- <vol_TIV>1402.50548259114</vol_TIV>
- <vol_rel_CGW>[0.152452206577022 0.485916659903727 0.361631133519251 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.58472295209548 0.627908989367132]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.59420228004456 0.808745335174631 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.99063128107836 0.255351737378285 0.306290185814533;2.62207603715158 0.17828045524699 0.416590440199502;3.27046879123326 0.276592895196419 0.277119373985965]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.845687457343126 0.389320457413221 0.575675382445481;4.28009704359655 0.385754547751111 0.424324617554519]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00014955861287</vol_TIV>
- <vol_rel_CGW>[0.587862905478126 6.57680782873074 4.34466834625091 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08073767026831</vol_rel_WMH>
- <surf_TSA>8.60438705225154</surf_TSA>
- <SQR>5.40229068403282</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.128951171875 1 1 8905.27671246435 0.410663022653364]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0268923006951809 0.0231046639382839 0.307324856519699]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[791.251402750383 472.020603023111 344.18149360483 1444.17446919467 2121.78222620408 5681.87108313091]</SPMvols0>
- <SPMvols1>[696.454652486344 445.618877761425 216.518436045977 1719.24627551087 1891.33467514256 5254.56905187036]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[313.904907226562 722.132019042969 961.046325683594]</T3th>
- <Tth>
- <T3th>[0 0 21.3796405792236 313.904907226562 722.132019042969 961.046325683594 1284.61706542969 3160.41259765625]</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>[0.0225123390555382 0.0872533395886421 0.0965872257947922 0 0]</dtc>
- <ll>[0.0846223804463192 0 0.0846223804463192 0;0.187333820246849 0.0116050749981389 0.198938895244988 2474.75903320312;0.187333820246849 0.0116050749981389 0.198938895244988 2474.75903320312]</ll>
- <rmsdtc>[0.0499635934829712 0.111057035624981 0.121563702821732]</rmsdtc>
- <rmsgdt>[0.0357145108282566 0.0452862456440926 0.0551267266273499]</rmsgdt>
- <rmsdt>0.121563702821732</rmsdt>
- <dt>0.0965872257947922</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>[0.0113878576084971 0.0442859828472137 0.062963142991066 0.0708979293704033 0.0761325508356094 0.0860103964805603]</dtc>
- <ll>[0.0839186762085097 0 0.0839186762085097 0;0.211569597069597 0.0167295863858364 0.228299183455433 8563.45703125;0.185731649430606 0.0189726240431068 0.204704273473712 13654.8251953125;0.16519336030241 0.0197456156992392 0.184938976001649 21291.14453125;0.148626699414012 0.0218690451198243 0.170495744533836 38256.6796875;0.148626699414012 0.0218690451198243 0.170495744533836 38256.6796875]</ll>
- <rmsdtc>[0.0132928444072604 0.0504060685634613 0.0745467022061348 0.100033588707447 0.120699048042297 0.127389892935753]</rmsdtc>
- <rmsgdt>[0.00355738704092801 0.0139956539496779 0.0294123236089945 0.0490760765969753 0.0657101273536682 0.070735476911068]</rmsgdt>
- <rmsdt>0.127389892935753</rmsdt>
- <dt>0.0860103964805603</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./ds/sub-f6950qp/sub-f6950qp_ses-wave1bas_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 74s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 14s</item>
- <item>Estimate background 12s</item>
- <item>Initial correction 15s</item>
- <item>Refine background 7s</item>
- <item>Final correction 13s</item>
- <item>Final scaling 15s</item>
- <item>91s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 16s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 153s</item>
- <item>SPM preprocessing 1 (estimate 2): 68s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 37s</item>
- <item>Update Segmentation 41s</item>
- <item>Update Skull-Stripping 95s</item>
- <item>Update probability maps 19s</item>
- <item>192s</item>
- <item>Global intensity correction: 36s</item>
- <item>SANLM denoising after intensity normalization (medium): 22s</item>
- <item>Fast Optimized Shooting registration 58s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 10s</item>
- <item>Prepare partitions 5s</item>
- <item>Prepare segments (LASmod = 1.00) 31s</item>
- <item>Estimate local tissue thresholds (WM) 39s</item>
- <item>Estimate local tissue thresholds (GM) 52s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 56s</item>
- <item>202s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 20s</item>
- <item>Major structures 8s</item>
- <item>Ventricle detection 29s</item>
- <item>Blood vessel detection 23s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 64s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 4s</item>
- <item>Side alignment 9s</item>
- <item>Final corrections 10s</item>
- <item>168s</item>
- <item>Blood vessel correction (BVCstr=0.50): 4s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 56s</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) 10s</item>
- <item>Level 1 cleanup (brain masking) 6s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 6s</item>
- <item>25s</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 | 0.0839 0.0000 0.0839 | 32.0000</item>
- <item>2 | 2.50 | 0.0804 0.0014 0.0818 | 29.4886</item>
- <item>3 | 2.50 | 0.0794 0.0022 0.0816 | 26.9772</item>
- <item>4 | 2.50 | 0.0788 0.0025 0.0813 | 24.6107</item>
- <item>5 | 2.50 | 0.0784 0.0027 0.0811 | 22.6548</item>
- <item>6 | 2.50 | 0.0780 0.0028 0.0809 | 20.6989</item>
- <item>7 | 2.50 | 0.0777 0.0030 0.0806 | 18.9688</item>
- <item>8 | 2.50 | 0.0773 0.0031 0.0804 | 17.4455</item>
- <item>9 | 2.50 | 0.0769 0.0032 0.0801 | 15.9223</item>
- <item>10 | 2.50 | 0.0765 0.0033 0.0798 | 14.6627</item>
- <item>11 | 2.50 | 0.0761 0.0035 0.0795 | 13.4764</item>
- <item>12 | 2.50 | 0.0756 0.0035 0.0792 | 12.3015</item>
- <item>13 | 2.50 | 0.0752 0.0037 0.0789 | 11.3776</item>
- <item>14 | 2.50 | 0.0748 0.0038 0.0785 | 10.4537</item>
- <item>15 | 2.25 | 0.0740 0.0039 0.0779 | 9.5920</item>
- <item>16 | 2.25 | 0.0705 0.0056 0.0761 | 8.8725</item>
- <item>29 | 2.00 | 0.0710 0.0025 0.0736 | 3.3283</item>
- <item>30 | 2.00 | 0.0642 0.0052 0.0695 | 3.1221</item>
- <item>31 | 2.00 | 0.0619 0.0063 0.0682 | 2.9160</item>
- <item>43 | 1.75 | 0.0606 0.0037 0.0643 | 1.5785</item>
- <item>44 | 1.75 | 0.0565 0.0058 0.0623 | 1.5194</item>
- <item>45 | 1.75 | 0.0551 0.0066 0.0616 | 1.4626</item>
- <item>57 | 1.50 | 0.0534 0.0049 0.0582 | 1.0900</item>
- <item>58 | 1.50 | 0.0505 0.0067 0.0572 | 1.0730</item>
- <item>59 | 1.50 | 0.0495 0.0073 0.0568 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 228s</item>
- <item>Prepare output 17s</item>
- <item>245s</item>
- <item>Jacobian determinant (RMS): 0.013 0.050 0.075 0.100 0.121 | 0.127390</item>
- <item>Template Matching: 0.084 0.212 0.186 0.165 0.149 | 0.148627</item>
- <item>Write result maps: 56s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 36s</item>
- <item>CSF distance: 20s</item>
- <item>PBT2x thickness: 55s</item>
- <item>119s</item>
- <item>Create initial surface 94s</item>
- <item>Topology correction: 101s</item>
- <item>Surface refinement: 105s</item>
- <item>Reduction of surface collisions with optimization: 60s</item>
- <item>Spherical mapping with areal smoothing 89s</item>
- <item>Spherical registration 298s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 18s</item>
- <item>PBT2x thickness: 54s</item>
- <item>119s</item>
- <item>Create initial surface 91s</item>
- <item>Topology correction: 101s</item>
- <item>Surface refinement: 84s</item>
- <item>Reduction of surface collisions with optimization: 63s</item>
- <item>Spherical mapping with areal smoothing 93s</item>
- <item>Spherical registration 302s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5849 0.6278 mm</item>
- <item>Surface intensity / position RMSE: 0.0705 / 0.0719</item>
- <item>Euler number / defect number / defect size: 14.0 / 4.5 / 0.40%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/surf/lh.thickness.sub-f6950qp_ses-wave1bas_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/surf/rh.thickness.sub-f6950qp_ses-wave1bas_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/sub-f6950qp_ses-wave1bas_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1858s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 30s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 114s</item>
- <item>ROI estimation of 'lpba40' atlas 34s</item>
- <item>ROI estimation of 'hammers' atlas 80s</item>
- <item>ROI estimation of 'thalamus' atlas 6s</item>
- <item>ROI estimation of 'ibsr' atlas 28s</item>
- <item>ROI estimation of 'aal3' atlas 44s</item>
- <item>ROI estimation of 'mori' atlas 66s</item>
- <item>ROI estimation of 'anatomy3' atlas 95s</item>
- <item>ROI estimation of 'julichbrain' atlas 125s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 46s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 55s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 203s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 300s</item>
- <item>Write results 301s</item>
- <item>1228s</item>
- <item>Quality check: 10s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/report/catreport_sub-f6950qp_ses-wave1bas_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 79 minute(s) and 9 second(s).</item>
- <item>Image Quality Rating (IQR): 86.64% (B)</item>
- <item>GM volume (GMV): 48.59% (681.50 / 1402.51 ml)</item>
- <item>GM thickness (GMT): 2.58 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_4103490/ds/sub-f6950qp/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|