123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.07178528955403 0.0228193445133241 0.0368863300301044 -3.07182018553974;-0.0019133869106443 0.952689988771286 0.353204325289622 -3.04507489506492;-0.030065809708588 -0.36399522330467 1.06497104912026 -24.3356264340722;0 0 0 1]</Affine>
- <Affine0>[1.07178528955403 0.0228193445133241 0.0368863300301044 -3.07182018553974;-0.0019133869106443 0.952689988771286 0.353204325289622 -3.04507489506492;-0.030065809708588 -0.36399522330467 1.06497104912026 -24.3356264340722;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[788.065280298876 1041.89805235314 333.193380629462 526.03089872449 277.744306710082 63.7463537661803 138.355674549482 1581.82262181752 850.977141988477 898.576636624132 571.589277143597 94.105016739119 1123.09031813872]</mn>
- <vr>[8911.14554170616;1510.43307037687;4669.4567927775;10921.7604663688;8269.12371445608;670.20687239967;2249.57416351504;228033.435308525;46240.4034537004;9115.99171148824;16216.6283121453;3829.76976420201;20058.7516425499]</vr>
- <ll>-6.41962385177612</ll>
- <Affine_translation>[-3.07182018553974 -3.04507489506492 -24.3356264340722]</Affine_translation>
- <Affine_rotation>[0.364354756155512 0.0268402871276129 -0.00832502928597117]</Affine_rotation>
- <Affine_scaling>[1.07220861816501 1.01963263174015 1.12150914525407]</Affine_scaling>
- <Affine_shearing>[0.0292079588659867 0.0059490310910667 -0.0485818813403137]</Affine_shearing>
- <Affine0_translation>[-3.07182018553974 -3.04507489506492 -24.3356264340722]</Affine0_translation>
- <Affine0_rotation>[0.364354756155512 0.0268402871276129 -0.00832502928597117]</Affine0_rotation>
- <Affine0_scaling>[1.07220861816501 1.01963263174015 1.12150914525407]</Affine0_scaling>
- <Affine0_shearing>[0.0292079588659867 0.0059490310910667 -0.0485818813403137]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_16809/ds/sub-season126</path>
- <file>sub-season126_ses-1_acq-MPrageHiRes_T1w</file>
- <fname>/var/lib/condor/execute/dir_16809/ds/sub-season126/sub-season126_ses-1_acq-MPrageHiRes_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_16809/ds/sub-season126/sub-season126_ses-1_acq-MPrageHiRes_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_16809/ds/sub-season126/mri/msub-season126_ses-1_acq-MPrageHiRes_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_16809/ds/sub-season126/mri/p0sub-season126_ses-1_acq-MPrageHiRes_T1w.nii</Fp0>
- <fnames>..s/sub-season126/..son126_ses-1_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>
- <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>8</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>
- </tr>
- <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>
- </tr>
- <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>
- </tr>
- <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>
- <affmod>0</affmod>
- <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>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- <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>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
- </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>
- <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>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>28</SurfaceEulerNumber>
- <SurfaceDefectArea>0.734064867032734</SurfaceDefectArea>
- <SurfaceDefectNumber>18</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.068381056189537</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0738864988088608</SurfacePositionRMSE>
- <res_vx_vol>[0.879996660799824 0.875000009050559 0.874999995868071]</res_vx_vol>
- <res_vx_voli>[0.879996659346966 0.875000005541243 0.874999997570108]</res_vx_voli>
- <res_RMS>0.876668719571698</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.77299976348877 289.932586669922 741.189392089844 1068.56359863281]</tissue_mn>
- <tissue_mnr>[0.00914592202752829 0.271329283714294 0.693631529808044 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[8.71229197884645 125.520264458228 98.1962593136656 62.3179173347582]</tissue_std>
- <tissue_stdr>[0.00822853110730648 0.118550598621368 0.0927437916398048 0.0588576383888721]</tissue_stdr>
- <contrast>330.395965576172</contrast>
- <contrastr>0.309196352958679</contrastr>
- <NCR>0.109799958765507</NCR>
- <ICR>0.278636664152145</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.75999332159965 1.75000001810112 1.74999999173614]</res_vx_vol>
- <res_RMS>1.7533374391434</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>3.44538807868958</contrastr>
- <NCR>1.90726327896118</NCR>
- <ICR>1.1508846282959</ICR>
- <SurfaceEulerNumber>2.3265306122449</SurfaceEulerNumber>
- <SurfaceDefectArea>1.18351621675818</SurfaceDefectArea>
- <SurfaceDefectNumber>1.9</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.36762118339539</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.47773003578186</SurfacePositionRMSE>
- <IQR>1.84143721830809</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>20220712-163001</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>28</SurfaceEulerNumber>
- <SurfaceDefectArea>0.734064867032734</SurfaceDefectArea>
- <SurfaceDefectNumber>18</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.068381056189537</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0738864988088608</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>28</EC_abs>
- <defect_size>0.734064867032734</defect_size>
- <vol_abs_CGW>[239.816299689857 710.2762186476 518.263209058307 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.21182593337384</vol_abs_WMH>
- <vol_rel_WMH>0.000825294518735662</vol_rel_WMH>
- <surf_TSA>2045.22101695357</surf_TSA>
- <vol_TIV>1468.35572739576</vol_TIV>
- <vol_rel_CGW>[0.163323025351076 0.483722169904514 0.352954804744409 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.46921103444596 0.574964971957413]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.47108745574951 0.707328620401823 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95227913921605 0.233642323499731 0.315881689864732;2.51453032845994 0.160785956104166 0.436697461282102;3.1104777933746 0.2510480268595 0.247420848853166]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.87977387467906 0.371496789404065 0.563747228381375;4.03501272974051 0.355128499421224 0.436252771618625]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.11051364238955</vol_TIV>
- <vol_rel_CGW>[0.783100311621345 6.53739529282532 4.1888434760131 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08252945187357</vol_rel_WMH>
- <surf_TSA>8.62272063648031</surf_TSA>
- <SQR>5.36481111204732</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.257960932595389 1 1 7339.25289077039 0.341905728605711]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00764550594612956 0 0.24876680970192]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[848.524565260466 460.644988123568 374.523139097184 1327.8903844314 3153.43514536271 4223.53516751387]</SPMvols0>
- <SPMvols1>[757.280859095794 435.688637686165 233.19258815935 1373.10089620371 2911.30705437695 4180.19315028245]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[365.418487548828 762.920227050781 1043.14111328125]</T3th>
- <Tth>
- <T3th>[0 0 15.268120765686 365.418487548828 762.920227050781 1043.14111328125 1382.00244140625 2865.67944335938]</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>[0.0228976365178823 0.0803206562995911 0.0884121134877205 0 0]</dtc>
- <ll>[0.0838489570632941 0 0.0838489570632941 0;0.190381932802418 0.0104622835157012 0.200844216318119 2231.06103515625;0.190381932802418 0.0104622835157012 0.200844216318119 2231.06103515625]</ll>
- <rmsdtc>[0.0477731786668301 0.102902486920357 0.112522713840008]</rmsdtc>
- <rmsgdt>[0.0337469652295113 0.0432085730135441 0.0527929775416851]</rmsgdt>
- <rmsdt>0.112522713840008</rmsdt>
- <dt>0.0884121134877205</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>[0.0112966224551201 0.0420581996440887 0.057656928896904 0.0649215430021286 0.0705748423933983 0.0788526237010956]</dtc>
- <ll>[0.0845721904673936 0 0.0845721904673936 0;0.216465537240537 0.0154257001678877 0.231891237408425 7896.0302734375;0.193581251945223 0.0172652747079735 0.210846526653196 12426.025390625;0.173843876475509 0.0185828611948098 0.192426737670319 20037.37890625;0.157189240107628 0.0212119963959532 0.178401236503582 37107.26953125;0.157189240107628 0.0212119963959532 0.178401236503582 37107.26953125]</ll>
- <rmsdtc>[0.0130456080660224 0.0474266186356544 0.0682178735733032 0.0906052216887474 0.110462561249733 0.116622976958752]</rmsdtc>
- <rmsgdt>[0.00342705519869924 0.0130563778802752 0.0277089960873127 0.0467983856797218 0.063236691057682 0.0684157535433769]</rmsgdt>
- <rmsdt>0.116622976958752</rmsdt>
- <dt>0.0788526237010956</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./sub-season126_ses-1_acq-MPrageHiRes_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 72s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 15s</item>
- <item>Refine background 3s</item>
- <item>Final correction 11s</item>
- <item>Final scaling 9s</item>
- <item>56s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 78s</item>
- <item>SPM preprocessing 1 (estimate 2): 80s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 16s</item>
- <item>Update Segmentation 19s</item>
- <item>Update Skull-Stripping 42s</item>
- <item>Update probability maps 8s</item>
- <item>85s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 14s</item>
- <item>Fast Optimized Shooting registration 29s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 14s</item>
- <item>Estimate local tissue thresholds (WM) 17s</item>
- <item>Estimate local tissue thresholds (GM) 24s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 27s</item>
- <item>92s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 13s</item>
- <item>Blood vessel detection 10s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.02) 28s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 5s</item>
- <item>74s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s</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) 4s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>11s</item>
- <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
- <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
- <item>1 | 2.50 | 0.0846 0.0000 0.0846 | 32.0000</item>
- <item>2 | 2.50 | 0.0813 0.0013 0.0827 | 29.4886</item>
- <item>3 | 2.50 | 0.0804 0.0021 0.0824 | 26.9772</item>
- <item>4 | 2.50 | 0.0799 0.0023 0.0822 | 24.6107</item>
- <item>5 | 2.50 | 0.0795 0.0025 0.0820 | 22.6548</item>
- <item>6 | 2.50 | 0.0792 0.0026 0.0818 | 20.6989</item>
- <item>7 | 2.50 | 0.0788 0.0027 0.0816 | 18.9688</item>
- <item>8 | 2.50 | 0.0785 0.0029 0.0813 | 17.4455</item>
- <item>9 | 2.50 | 0.0781 0.0029 0.0810 | 15.9223</item>
- <item>10 | 2.50 | 0.0777 0.0031 0.0808 | 14.6627</item>
- <item>11 | 2.50 | 0.0773 0.0032 0.0805 | 13.4764</item>
- <item>12 | 2.50 | 0.0769 0.0032 0.0802 | 12.3015</item>
- <item>13 | 2.50 | 0.0765 0.0034 0.0799 | 11.3776</item>
- <item>14 | 2.50 | 0.0762 0.0034 0.0796 | 10.4537</item>
- <item>15 | 2.25 | 0.0754 0.0036 0.0790 | 9.5920</item>
- <item>16 | 2.25 | 0.0722 0.0051 0.0773 | 8.8725</item>
- <item>29 | 2.00 | 0.0727 0.0023 0.0751 | 3.3283</item>
- <item>30 | 2.00 | 0.0666 0.0048 0.0714 | 3.1221</item>
- <item>31 | 2.00 | 0.0645 0.0058 0.0703 | 2.9160</item>
- <item>43 | 1.75 | 0.0634 0.0033 0.0667 | 1.5785</item>
- <item>44 | 1.75 | 0.0593 0.0055 0.0648 | 1.5194</item>
- <item>45 | 1.75 | 0.0579 0.0062 0.0641 | 1.4626</item>
- <item>57 | 1.50 | 0.0563 0.0045 0.0609 | 1.0900</item>
- <item>58 | 1.50 | 0.0534 0.0064 0.0598 | 1.0730</item>
- <item>59 | 1.50 | 0.0524 0.0071 0.0595 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 134s</item>
- <item>Prepare output 9s</item>
- <item>143s</item>
- <item>Jacobian determinant (RMS): 0.013 0.047 0.068 0.091 0.110 | 0.116623</item>
- <item>Template Matching: 0.085 0.216 0.194 0.174 0.157 | 0.157189</item>
- <item>Write result maps: 25s</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: 12s</item>
- <item>PBT2x thickness: 36s</item>
- <item>84s</item>
- <item>Create initial surface 58s</item>
- <item>Topology correction: 65s</item>
- <item>Surface refinement: 75s</item>
- <item>Reduction of surface collisions with optimization: 43s</item>
- <item>Spherical mapping with areal smoothing 61s</item>
- <item>Spherical registration 178s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 31s</item>
- <item>CSF distance: 13s</item>
- <item>PBT2x thickness: 36s</item>
- <item>85s</item>
- <item>Create initial surface 58s</item>
- <item>Topology correction: 65s</item>
- <item>Surface refinement: 72s</item>
- <item>Reduction of surface collisions with optimization: 44s</item>
- <item>Spherical mapping with areal smoothing 60s</item>
- <item>Spherical registration 164s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4692 0.5750 mm</item>
- <item>Surface intensity / position RMSE: 0.0684 / 0.0739</item>
- <item>Euler number / defect number / defect size: 28.0 / 18.0 / 0.73%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_16809/ds/sub-season126/surf/lh.thickness.sub-season126_ses-1_acq-MPrageHiRes_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_16809/ds/sub-season126/surf/rh.thickness.sub-season126_ses-1_acq-MPrageHiRes_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_16809/ds/sub-season126/sub-season126_ses-1_acq-MPrageHiRes_T1w.nii</item>
- <item>Surface ROI estimation: 5s</item>
- <item>Surface and thickness estimation takes: 1193s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 47s</item>
- <item>ROI estimation of 'lpba40' atlas 14s</item>
- <item>ROI estimation of 'hammers' atlas 34s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 19s</item>
- <item>ROI estimation of 'mori' atlas 28s</item>
- <item>ROI estimation of 'anatomy3' atlas 40s</item>
- <item>ROI estimation of 'julichbrain' atlas 53s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 19s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 87s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 126s</item>
- <item>Write results 126s</item>
- <item>519s</item>
- <item>Quality check: 5s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_16809/ds/sub-season126/report/catreport_sub-season126_ses-1_acq-MPrageHiRes_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 43 minute(s) and 47 second(s).</item>
- <item>Image Quality Rating (IQR): 86.59% (B)</item>
- <item>GM volume (GMV): 48.37% (710.28 / 1468.36 ml)</item>
- <item>GM thickness (GMT): 2.47 0.57 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_16809/ds/sub-season126/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_16809/ds/sub-season126/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_16809/ds/sub-season126/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|