123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.0368315244174 -0.014130021558122 -0.0883173576364338 1.29602701297261;0.0701326947164044 1.03955021733703 0.280452390754595 -18.3447286232992;0.0869888413003092 -0.319728101904613 1.12170158875166 7.01060033929925;0 0 0 1]</Affine>
- <Affine0>[1.0368315244174 -0.014130021558122 -0.0883173576364338 1.29602701297261;0.0701326947164044 1.03955021733703 0.280452390754595 -18.3447286232992;0.0869888413003092 -0.319728101904613 1.12170158875166 7.01060033929925;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[213.835566855781 298.829699669724 68.36491886675 126.709969348828 154.881670428195 31.7085248823472 54.7645254971285 260.319345344397 499.726719237468 379.302976516017 219.368934895171 168.411171842134 31.8171864148514]</mn>
- <vr>[953.349207589014;191.196451071557;371.256110518022;1182.94227586589;4121.21331887202;63.5241977936232;290.169347149492;3467.32254264459;1731.0176541654;7377.44746441537;415.071150588225;2295.42531008182;144.955760896649]</vr>
- <ll>-5.41901016235352</ll>
- <Affine_translation>[1.29602701297261 -18.3447286232992 7.01060033929925]</Affine_translation>
- <Affine_rotation>[0.297082110921183 -0.0996926774101578 -0.0398981408983416]</Affine_rotation>
- <Affine_scaling>[1.04283520433704 1.08730775508759 1.15771923611994]</Affine_scaling>
- <Affine_shearing>[0.0279936384230201 0.0236083297311332 -0.0563050376074]</Affine_shearing>
- <Affine0_translation>[1.29602701297261 -18.3447286232992 7.01060033929925]</Affine0_translation>
- <Affine0_rotation>[0.297082110921183 -0.0996926774101578 -0.0398981408983416]</Affine0_rotation>
- <Affine0_scaling>[1.04283520433704 1.08730775508759 1.15771923611994]</Affine0_scaling>
- <Affine0_shearing>[0.0279936384230201 0.0236083297311332 -0.0563050376074]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2</path>
- <file>sub-0026128_ses-2_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/sub-0026128_ses-2_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/sub-0026128_ses-2_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/mri/msub-0026128_ses-2_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/mri/p0sub-0026128_ses-2_run-1_T1w.nii</Fp0>
- <fnames>..4/ds/UM/sub-0026128/ses-2/sub-0026128_ses-2_run-1_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_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</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>
- <tr>
- <td>/var/lib/condor/execute/dir_2298364/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</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>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.350712786848629</SurfaceDefectArea>
- <SurfaceDefectNumber>10</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0633306354284286</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0614666119217873</SurfacePositionRMSE>
- <res_vx_vol>[1.00000004061292 0.999999992791919 1.00000002844357]</res_vx_vol>
- <res_vx_voli>[1.00000010059553 0.999999997860863 1.00000002962928]</res_vx_voli>
- <res_RMS>1.00000002061614</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 70.9710006713867 197.039993286133 310.894012451172]</tissue_mn>
- <tissue_mnr>[0 0.228280365467072 0.633785128593445 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[14.437080728819 31.9730173652587 34.1169640804334 21.5670267308117]</tissue_std>
- <tissue_stdr>[0.0464373081922531 0.102842174470425 0.109738245606422 0.0693709924817085]</tissue_stdr>
- <contrast>111.949935913086</contrast>
- <contrastr>0.360090345144272</contrastr>
- <res_ECR>0.383210182189941</res_ECR>
- <NCR>0.172261074185371</NCR>
- <ICR>0.242855027318001</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000008122585 1.99999998558384 2.00000005688715]</res_vx_vol>
- <res_RMS>2.00000004123228</res_RMS>
- <res_ECR>2.85311317443848</res_ECR>
- <res_BB>1</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>2.68197822570801</contrastr>
- <NCR>2.80392026901245</NCR>
- <ICR>1.06214046478271</ICR>
- <SurfaceEulerNumber>1.51020408163265</SurfaceEulerNumber>
- <SurfaceDefectArea>1.08767819671216</SurfaceDefectArea>
- <SurfaceDefectNumber>1.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.26661276817322</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.22933220863342</SurfacePositionRMSE>
- <SIQR>2.69978256650255</SIQR>
- <IQR>2.59213595821577</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
- <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>2040</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>20231031-014834</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>12</SurfaceEulerNumber>
- <SurfaceDefectArea>0.350712786848629</SurfaceDefectArea>
- <SurfaceDefectNumber>10</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0633306354284286</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0614666119217873</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>12</EC_abs>
- <defect_size>0.350712786848629</defect_size>
- <vol_abs_CGW>[269.791744360376 631.186884767559 466.913440197075 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.68734126450915</vol_abs_WMH>
- <vol_rel_WMH>0.000502482088991363</vol_rel_WMH>
- <surf_TSA>1806.0405792243</surf_TSA>
- <vol_TIV>1367.89206932501</vol_TIV>
- <vol_rel_CGW>[0.197231748330485 0.46143032694021 0.341337924729306 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.51866344350846 0.610427314774961]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.49540305137634 0.762987527619312 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95891200316241 0.244852688145869 0.324471599539544;2.55388245166482 0.174408250927106 0.440498327781978;3.22593521987315 0.280080687026186 0.235030072678478]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.921370354274983 0.332043741833987 0.506198781256566;4.23370572490895 0.358988951072929 0.493801218743433]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.02452212850116</vol_TIV>
- <vol_rel_CGW>[1.39209318122278 6.13703891774802 3.98020698148897 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05024820889914</vol_rel_WMH>
- <surf_TSA>8.58798518701654</surf_TSA>
- <SQR>5.03803565371181</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10813.4406687942 0.395218299094122]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00136932148598135 0.00122335879132152 0.0429827198386192]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[741.151232185749 425.349309383109 445.196060944801 2741.87544531258 685.849550592593 6641.81427032903]</SPMvols0>
- <SPMvols1>[654.876444664598 402.152573078606 267.235293052539 889.147835455718 631.803798572067 7970.16382086372]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[77.1992034912109 206.014099121094 299.784301757812]</T3th>
- <Tth>
- <T3th>[-4.28595018386841 -4.28595399856567 3.86979746818542 77.1992034912109 206.014099121094 299.784301757812 411.076843261719 704.727355957031]</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>[0.0244609359651804 0.0935401245951653 0.105309516191483 0 0]</dtc>
- <ll>[0.0887207727329213 0 0.0887207727329213 0;0.195848334450968 0.0134223649481765 0.209270699399144 2862.29248046875;0.195848334450968 0.0134223649481765 0.209270699399144 2862.29248046875]</ll>
- <rmsdtc>[0.052157673984766 0.123544842004776 0.136917904019356]</rmsdtc>
- <rmsgdt>[0.0368070490658283 0.0528881885111332 0.0651991367340088]</rmsgdt>
- <rmsdt>0.136917904019356</rmsdt>
- <dt>0.105309516191483</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>[0.0119859799742699 0.0482138320803642 0.0659105628728867 0.0744607821106911 0.0803344398736954 0.0922772288322449]</dtc>
- <ll>[0.0888379603280467 0 0.0888379603280467 0;0.223879395604396 0.019912799526862 0.243792195131258 10192.8642578125;0.200996674711551 0.0207706957023261 0.221767370413877 14948.9189453125;0.178716255615466 0.0216900480438841 0.20040630365935 23387.771484375;0.161421429808621 0.0242973044891454 0.185718734297766 42504.5625;0.161421429808621 0.0242973044891454 0.185718734297766 42504.5625]</ll>
- <rmsdtc>[0.0140899615362287 0.0529250800609589 0.0808999612927437 0.109667390584946 0.135633111000061 0.143210202455521]</rmsdtc>
- <rmsgdt>[0.00377589045092463 0.0151671627536416 0.0331414677202702 0.0561723262071609 0.0760250017046928 0.081571526825428]</rmsgdt>
- <rmsdt>0.143210202455521</rmsdt>
- <dt>0.0922772288322449</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026128/ses-2/sub-0026128_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 36s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>26s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 59s</item>
- <item>SPM preprocessing 1 (estimate 2): 60s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 13s</item>
- <item>Update Segmentation 14s</item>
- <item>Update Skull-Stripping 30s</item>
- <item>Update probability maps 7s</item>
- <item>63s</item>
- <item>Global intensity correction: 11s</item>
- <item>SANLM denoising after intensity normalization (medium): 19s</item>
- <item>Fast Optimized Shooting registration 26s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.11) 10s</item>
- <item>Estimate local tissue thresholds (WM) 13s</item>
- <item>Estimate local tissue thresholds (GM) 19s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 28s</item>
- <item>77s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 6s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 8s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 15s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 3s</item>
- <item>44s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 25s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.04]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 3s</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>8s</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 | 0.0888 0.0000 0.0888 | 32.0000</item>
- <item>2 | 2.50 | 0.0852 0.0015 0.0867 | 29.4886</item>
- <item>3 | 2.50 | 0.0841 0.0023 0.0864 | 26.9772</item>
- <item>4 | 2.50 | 0.0836 0.0026 0.0862 | 24.6107</item>
- <item>5 | 2.50 | 0.0831 0.0028 0.0860 | 22.6548</item>
- <item>6 | 2.50 | 0.0827 0.0030 0.0857 | 20.6989</item>
- <item>7 | 2.50 | 0.0823 0.0031 0.0854 | 18.9688</item>
- <item>8 | 2.50 | 0.0819 0.0033 0.0852 | 17.4455</item>
- <item>9 | 2.50 | 0.0815 0.0034 0.0849 | 15.9223</item>
- <item>10 | 2.50 | 0.0810 0.0036 0.0846 | 14.6627</item>
- <item>11 | 2.50 | 0.0806 0.0037 0.0843 | 13.4764</item>
- <item>12 | 2.50 | 0.0801 0.0038 0.0839 | 12.3015</item>
- <item>13 | 2.50 | 0.0796 0.0039 0.0836 | 11.3776</item>
- <item>14 | 2.50 | 0.0792 0.0040 0.0832 | 10.4537</item>
- <item>15 | 2.25 | 0.0797 0.0042 0.0839 | 9.5920</item>
- <item>16 | 2.25 | 0.0761 0.0060 0.0821 | 8.8725</item>
- <item>17 | 2.25 | 0.0746 0.0066 0.0813 | 8.1530</item>
- <item>29 | 2.00 | 0.0758 0.0030 0.0789 | 3.3283</item>
- <item>30 | 2.00 | 0.0693 0.0058 0.0751 | 3.1221</item>
- <item>31 | 2.00 | 0.0670 0.0069 0.0739 | 2.9160</item>
- <item>43 | 1.75 | 0.0656 0.0040 0.0696 | 1.5785</item>
- <item>44 | 1.75 | 0.0611 0.0064 0.0675 | 1.5194</item>
- <item>45 | 1.75 | 0.0596 0.0072 0.0668 | 1.4626</item>
- <item>57 | 1.50 | 0.0581 0.0053 0.0634 | 1.0900</item>
- <item>58 | 1.50 | 0.0549 0.0074 0.0623 | 1.0730</item>
- <item>59 | 1.50 | 0.0538 0.0081 0.0619 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 130s</item>
- <item>Prepare output 7s</item>
- <item>137s</item>
- <item>Jacobian determinant (RMS): 0.014 0.053 0.081 0.110 0.136 | 0.143210</item>
- <item>Template Matching: 0.089 0.224 0.201 0.179 0.161 | 0.161421</item>
- <item>Write result maps: 29s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 26s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 30s</item>
- <item>71s</item>
- <item>Create initial surface 55s</item>
- <item>Topology correction: 69s</item>
- <item>Surface refinement: 75s</item>
- <item>Reduction of surface collisions with optimization: 46s</item>
- <item>Spherical mapping with areal smoothing 89s</item>
- <item>Spherical registration 207s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 19s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 30s</item>
- <item>64s</item>
- <item>Create initial surface 53s</item>
- <item>Topology correction: 66s</item>
- <item>Surface refinement: 50s</item>
- <item>Reduction of surface collisions with optimization: 44s</item>
- <item>Spherical mapping with areal smoothing 62s</item>
- <item>Spherical registration 211s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5187 0.6104 mm</item>
- <item>Surface intensity / position RMSE: 0.0633 / 0.0615</item>
- <item>Euler number / defect number / defect size: 12.0 / 10.0 / 0.35%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/surf/lh.thickness.sub-0026128_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/surf/rh.thickness.sub-0026128_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/sub-0026128_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1231s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 26s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 18s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 10s</item>
- <item>ROI estimation of 'mori' atlas 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 22s</item>
- <item>ROI estimation of 'julichbrain' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 22s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 48s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 75s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 7s</item>
- <item>308s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/report/catreport_sub-0026128_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 37 minute(s) and 32 second(s).</item>
- <item>Image Quality Rating (IQR): 79.08% (C+)</item>
- <item>GM volume (GMV): 46.14% (631.19 / 1367.89 ml)</item>
- <item>GM thickness (GMT): 2.52 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2298364/ds/UM/sub-0026128/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|