123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.06383334545293 -0.0527809861264616 -0.093820295414138 -5.9687794548394;0.0999689243022308 1.04161731622142 0.314119861053748 -24.312734393782;0.0918886969168292 -0.302909077733693 1.17126714160935 -15.8575335264192;0 0 0 1]</Affine>
- <Affine0>[1.06383334545293 -0.0527809861264616 -0.093820295414138 -5.9687794548394;0.0999689243022308 1.04161731622142 0.314119861053748 -24.312734393782;0.0918886969168292 -0.302909077733693 1.17126714160935 -15.8575335264192;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[240.123445963594 340.987326562182 77.1475563479647 139.354881051024 130.590189199263 39.0483539268688 68.0503936804157 289.886317227002 574.952615804752 438.218076285118 232.238724035886 178.373183738903 31.4367112744026]</mn>
- <vr>[1332.04483213367;240.380044803876;480.217838050589;1462.52530986405;1837.16831470174;94.0234339505855;415.972238496122;3539.49612171777;1698.12229049411;9641.19522162762;731.973509236155;3250.51397589202;67.9246076292803]</vr>
- <ll>-5.55802440643311</ll>
- <Affine_translation>[-5.9687794548394 -24.312734393782 -15.8575335264192]</Affine_translation>
- <Affine_rotation>[0.27770598412582 -0.10840120895893 -0.0662020857037642]</Affine_rotation>
- <Affine_scaling>[1.07246384803628 1.08588836114721 1.21554158844984]</Affine_scaling>
- <Affine_shearing>[0.0175149036051292 0.0340984205945026 -0.0197851734328957]</Affine_shearing>
- <Affine0_translation>[-5.9687794548394 -24.312734393782 -15.8575335264192]</Affine0_translation>
- <Affine0_rotation>[0.27770598412582 -0.10840120895893 -0.0662020857037642]</Affine0_rotation>
- <Affine0_scaling>[1.07246384803628 1.08588836114721 1.21554158844984]</Affine0_scaling>
- <Affine0_shearing>[0.0175149036051292 0.0340984205945026 -0.0197851734328957]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2</path>
- <file>sub-0026138_ses-2_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/sub-0026138_ses-2_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/sub-0026138_ses-2_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/mri/msub-0026138_ses-2_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/mri/p0sub-0026138_ses-2_run-1_T1w.nii</Fp0>
- <fnames>..4/ds/UM/sub-0026138/ses-2/sub-0026138_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_3618454/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>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0853228972543077</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0653223544359207</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0619054362177849</SurfacePositionRMSE>
- <res_vx_vol>[0.999999982111135 0.999999983725053 1.00000000245362]</res_vx_vol>
- <res_vx_voli>[1.00000003871356 0.999999983867237 1.0000000001536]</res_vx_voli>
- <res_RMS>0.999999989429936</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[10.9770002365112 81.6589965820312 218.651000976562 352.178985595703]</tissue_mn>
- <tissue_mnr>[0.0311688110232353 0.231867879629135 0.620851933956146 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[8.05511688930063 35.8135895126522 38.6683464512999 25.2995546093056]</tissue_std>
- <tissue_stdr>[0.0236080586910248 0.104963012039661 0.113329775631428 0.0741483196616173]</tissue_stdr>
- <contrast>125.04613494873</contrast>
- <contrastr>0.355064153671265</contrastr>
- <res_ECR>0.398692071437836</res_ECR>
- <NCR>0.173828184604645</NCR>
- <ICR>0.254911631345749</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999996422227 1.99999996745011 2.00000000490724]</res_vx_vol>
- <res_RMS>1.99999997885987</res_RMS>
- <res_ECR>2.93210220336914</res_ECR>
- <res_BB>1</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>2.7573709487915</contrastr>
- <NCR>2.82641673088074</NCR>
- <ICR>1.09204268455505</ICR>
- <SurfaceEulerNumber>1.30612244897959</SurfaceEulerNumber>
- <SurfaceDefectArea>1.02133072431358</SurfaceDefectArea>
- <SurfaceDefectNumber>1.425</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.30644702911377</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.23810875415802</SurfacePositionRMSE>
- <SIQR>2.74927125067838</SIQR>
- <IQR>2.61166083386481</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>20231031-023111</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>8</SurfaceEulerNumber>
- <SurfaceDefectArea>0.0853228972543077</SurfaceDefectArea>
- <SurfaceDefectNumber>8.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0653223544359207</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0619054362177849</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>8</EC_abs>
- <defect_size>0.0853228972543077</defect_size>
- <vol_abs_CGW>[251.304727281889 592.246350719266 439.705080584665 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.10134904464635</vol_abs_WMH>
- <vol_rel_WMH>0.000858245672368379</vol_rel_WMH>
- <surf_TSA>1696.52232633457</surf_TSA>
- <vol_TIV>1283.25615858582</vol_TIV>
- <vol_rel_CGW>[0.195833642099044 0.461518416846669 0.342647941054287 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.45120936213562 0.630963471722475]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.42417573928833 0.809422355209226 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.85821765222338 0.270566645928581 0.321775251421076;2.48515938895995 0.183099858650209 0.453884273429529;3.20237505245692 0.297972789612915 0.224340475149395]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.810792125005896 0.252291367767027 0.510855829982769;4.27167959933328 0.357111189438376 0.489144170017231]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.31789607951419</vol_TIV>
- <vol_rel_CGW>[1.36698351470983 6.13862099221748 4.00373457353246 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.08582456723684</vol_rel_WMH>
- <surf_TSA>8.49706786455026</surf_TSA>
- <SQR>5.04021505975738</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10813.4396571038 0.420231582554833]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00128453597426414 0.001092966995202 0.0470287129282951]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[710.804408316573 392.112550090913 416.969472224648 1261.64131887873 700.32509827441 7879.38725364293]</SPMvols0>
- <SPMvols1>[633.19347714037 371.516922171704 236.331946549335 658.259920847496 654.908822732095 8259.86716425369]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[87.5510025024414 231.078506469727 341.887512207031]</T3th>
- <Tth>
- <T3th>[-4.88176012039185 -4.88176250457764 4.296302318573 87.5510025024414 231.078506469727 341.887512207031 469.055786132812 810.960571289062]</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>[0.0228696130216122 0.0846620872616768 0.0942774638533592 0 0]</dtc>
- <ll>[0.0855552670286865 0 0.0855552670286865 0;0.193544733567255 0.0115807431370986 0.205125476704354 2469.5703125;0.193544733567255 0.0115807431370986 0.205125476704354 2469.5703125]</ll>
- <rmsdtc>[0.048647865653038 0.11126221716404 0.122967340052128]</rmsdtc>
- <rmsgdt>[0.0344208404421806 0.0480956509709358 0.0595380552113056]</rmsgdt>
- <rmsdt>0.122967340052128</rmsdt>
- <dt>0.0942774638533592</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>[0.0110583398491144 0.041487067937851 0.058781124651432 0.0665420666337013 0.0725301653146744 0.0824151337146759]</dtc>
- <ll>[0.0865323724365975 0 0.0865323724365975 0;0.223542200854701 0.0157535208714896 0.23929572172619 8063.83349609375;0.200607282843693 0.0180953254240064 0.218702608267699 13023.4228515625;0.179587354234368 0.0196343482616167 0.199221702495984 21171.16796875;0.162643667401605 0.0225241355303932 0.185167802931998 39402.6640625;0.162643667401605 0.0225241355303932 0.185167802931998 39402.6640625]</ll>
- <rmsdtc>[0.0130733046680689 0.048193734139204 0.0713171809911728 0.0973607525229454 0.121077217161655 0.128751710057259]</rmsdtc>
- <rmsgdt>[0.0034274582285434 0.013588260859251 0.0296813677996397 0.0512576960027218 0.0701789930462837 0.0760956555604935]</rmsgdt>
- <rmsdt>0.128751710057259</rmsdt>
- <dt>0.0824151337146759</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026138/ses-2/sub-0026138_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 34s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 4s</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>23s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 48s</item>
- <item>SPM preprocessing 1 (estimate 2): 56s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 11s</item>
- <item>Update Segmentation 13s</item>
- <item>Update Skull-Stripping 28s</item>
- <item>Update probability maps 6s</item>
- <item>58s</item>
- <item>Global intensity correction: 10s</item>
- <item>SANLM denoising after intensity normalization (medium): 17s</item>
- <item>Fast Optimized Shooting registration 23s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 1s</item>
- <item>Prepare segments (LASmod = 1.00) 9s</item>
- <item>Estimate local tissue thresholds (WM) 11s</item>
- <item>Estimate local tissue thresholds (GM) 16s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 26s</item>
- <item>69s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 5s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 7s</item>
- <item>Blood vessel detection 5s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.07) 13s</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>38s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 22s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 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>7s</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 | 0.0865 0.0000 0.0865 | 32.0000</item>
- <item>2 | 2.50 | 0.0834 0.0013 0.0848 | 29.4886</item>
- <item>3 | 2.50 | 0.0825 0.0021 0.0846 | 26.9772</item>
- <item>4 | 2.50 | 0.0820 0.0024 0.0844 | 24.6107</item>
- <item>5 | 2.50 | 0.0816 0.0025 0.0842 | 22.6548</item>
- <item>6 | 2.50 | 0.0813 0.0027 0.0839 | 20.6989</item>
- <item>7 | 2.50 | 0.0809 0.0028 0.0837 | 18.9688</item>
- <item>8 | 2.50 | 0.0806 0.0029 0.0835 | 17.4455</item>
- <item>9 | 2.50 | 0.0802 0.0030 0.0832 | 15.9223</item>
- <item>10 | 2.50 | 0.0798 0.0032 0.0830 | 14.6627</item>
- <item>11 | 2.50 | 0.0794 0.0033 0.0827 | 13.4764</item>
- <item>12 | 2.50 | 0.0790 0.0034 0.0824 | 12.3015</item>
- <item>13 | 2.50 | 0.0786 0.0035 0.0821 | 11.3776</item>
- <item>14 | 2.50 | 0.0782 0.0036 0.0818 | 10.4537</item>
- <item>15 | 2.25 | 0.0777 0.0037 0.0814 | 9.5920</item>
- <item>16 | 2.25 | 0.0745 0.0053 0.0798 | 8.8725</item>
- <item>29 | 2.00 | 0.0756 0.0024 0.0780 | 3.3283</item>
- <item>30 | 2.00 | 0.0691 0.0050 0.0741 | 3.1221</item>
- <item>31 | 2.00 | 0.0669 0.0060 0.0729 | 2.9160</item>
- <item>43 | 1.75 | 0.0655 0.0035 0.0690 | 1.5785</item>
- <item>44 | 1.75 | 0.0613 0.0057 0.0671 | 1.5194</item>
- <item>45 | 1.75 | 0.0599 0.0065 0.0664 | 1.4626</item>
- <item>57 | 1.50 | 0.0584 0.0048 0.0632 | 1.0900</item>
- <item>58 | 1.50 | 0.0553 0.0068 0.0621 | 1.0730</item>
- <item>59 | 1.50 | 0.0542 0.0075 0.0617 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 115s</item>
- <item>Prepare output 7s</item>
- <item>122s</item>
- <item>Jacobian determinant (RMS): 0.013 0.048 0.071 0.097 0.121 | 0.128752</item>
- <item>Template Matching: 0.087 0.224 0.201 0.180 0.163 | 0.162644</item>
- <item>Write result maps: 24s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 17s</item>
- <item>CSF distance: 9s</item>
- <item>PBT2x thickness: 26s</item>
- <item>55s</item>
- <item>Create initial surface 47s</item>
- <item>Topology correction: 49s</item>
- <item>Surface refinement: 44s</item>
- <item>Reduction of surface collisions with optimization: 36s</item>
- <item>Spherical mapping with areal smoothing 51s</item>
- <item>Spherical registration 197s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 16s</item>
- <item>CSF distance: 9s</item>
- <item>PBT2x thickness: 26s</item>
- <item>55s</item>
- <item>Create initial surface 46s</item>
- <item>Topology correction: 50s</item>
- <item>Surface refinement: 44s</item>
- <item>Reduction of surface collisions with optimization: 37s</item>
- <item>Spherical mapping with areal smoothing 51s</item>
- <item>Spherical registration 203s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4512 0.6307 mm</item>
- <item>Surface intensity / position RMSE: 0.0653 / 0.0619</item>
- <item>Euler number / defect number / defect size: 8.0 / 8.5 / 0.09%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/surf/lh.thickness.sub-0026138_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/surf/rh.thickness.sub-0026138_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/sub-0026138_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1026s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 27s</item>
- <item>ROI estimation of 'lpba40' atlas 8s</item>
- <item>ROI estimation of 'hammers' atlas 19s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 7s</item>
- <item>ROI estimation of 'aal3' atlas 11s</item>
- <item>ROI estimation of 'mori' atlas 18s</item>
- <item>ROI estimation of 'anatomy3' atlas 25s</item>
- <item>ROI estimation of 'julichbrain' atlas 33s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 50s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 70s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 7s</item>
- <item>320s</item>
- <item>Quality check: 8s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/report/catreport_sub-0026138_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 32 minute(s) and 54 second(s).</item>
- <item>Image Quality Rating (IQR): 78.88% (C+)</item>
- <item>GM volume (GMV): 46.15% (592.25 / 1283.26 ml)</item>
- <item>GM thickness (GMT): 2.45 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3618454/ds/UM/sub-0026138/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|