123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699700701702703 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.03301778412125 0.0112034480992732 -0.0331548066984844 -2.95776304961133;-0.00576065875607064 1.01594172682001 0.385004817753507 -19.6756045238568;0.0428584674578788 -0.397582373882919 1.1070979267196 -8.5224456574309;0 0 0 1]</Affine>
- <Affine0>[1.03301778412125 0.0112034480992732 -0.0331548066984844 -2.95776304961133;-0.00576065875607064 1.01594172682001 0.385004817753507 -19.6756045238568;0.0428584674578788 -0.397582373882919 1.1070979267196 -8.5224456574309;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[252.080425868389 342.201535642831 84.1253936062809 157.630736800144 238.939312383793 48.4938517772001 107.055349120735 335.158703533754 566.593770038259 421.182586520392 240.942128301189 184.051997061059 36.3518096982042]</mn>
- <vr>[1208.23957012283;286.510464668982;538.569921029808;1742.32640253802;5056.1199219427;159.152259129158;1567.22434917047;5809.78667333088;2631.24831455736;13375.2627178964;1216.75718567869;4737.12627281023;120.238618949964]</vr>
- <ll>-5.6486554145813</ll>
- <Affine_translation>[-2.95776304961133 -19.6756045238568 -8.5224456574309]</Affine_translation>
- <Affine_rotation>[0.373397640576482 -0.0365792263846713 0.0203101403095984]</Affine_rotation>
- <Affine_scaling>[1.03392251921163 1.09096975440544 1.17168295656889]</Affine_scaling>
- <Affine_shearing>[-0.0105883521376513 0.0102723831011498 -0.0414003673926977]</Affine_shearing>
- <Affine0_translation>[-2.95776304961133 -19.6756045238568 -8.5224456574309]</Affine0_translation>
- <Affine0_rotation>[0.373397640576482 -0.0365792263846713 0.0203101403095984]</Affine0_rotation>
- <Affine0_scaling>[1.03392251921163 1.09096975440544 1.17168295656889]</Affine0_scaling>
- <Affine0_shearing>[-0.0105883521376513 0.0102723831011498 -0.0414003673926977]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2</path>
- <file>sub-0026189_ses-2_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/sub-0026189_ses-2_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/sub-0026189_ses-2_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/mri/msub-0026189_ses-2_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/mri/p0sub-0026189_ses-2_run-1_T1w.nii</Fp0>
- <fnames>..3/ds/UM/sub-0026189/ses-2/sub-0026189_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_3556103/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>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.476836043085162</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0626756325364113</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0609335899353027</SurfacePositionRMSE>
- <res_vx_vol>[0.99999994225197 0.999999961873259 0.999999980848735]</res_vx_vol>
- <res_vx_voli>[1.00000000016127 0.999999960835745 0.999999981403096]</res_vx_voli>
- <res_RMS>0.999999961657988</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[0 81.3850021362305 229.610000610352 352.679992675781]</tissue_mn>
- <tissue_mnr>[0 0.230761602520943 0.651043474674225 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[10.3366973004942 38.205440154911 38.4610581854749 24.5020553408332]</tissue_std>
- <tissue_stdr>[0.0293089989572763 0.10832891613245 0.109053701162338 0.0694738999009132]</tissue_stdr>
- <contrast>123.06999206543</contrast>
- <contrastr>0.348956555128098</contrastr>
- <res_ECR>0.404179990291595</res_ECR>
- <NCR>0.20141389966011</NCR>
- <ICR>0.30087074637413</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99999988450394 1.99999992374652 1.99999996169747]</res_vx_vol>
- <res_RMS>1.99999992331598</res_RMS>
- <res_ECR>2.96010184288025</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>2.84898495674133</contrastr>
- <NCR>3.22242164611816</NCR>
- <ICR>1.20602869987488</ICR>
- <SurfaceEulerNumber>1.81632653061224</SurfaceEulerNumber>
- <SurfaceDefectArea>1.11920901077129</SurfaceDefectArea>
- <SurfaceDefectNumber>1.775</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.2535126209259</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.21867179870605</SurfacePositionRMSE>
- <SIQR>2.96205571595137</SIQR>
- <IQR>2.96302927928924</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>20231031-014849</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>18</SurfaceEulerNumber>
- <SurfaceDefectArea>0.476836043085162</SurfaceDefectArea>
- <SurfaceDefectNumber>15.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0626756325364113</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0609335899353027</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>18</EC_abs>
- <defect_size>0.476836043085162</defect_size>
- <vol_abs_CGW>[304.62835500246 637.622931900441 470.285619970424 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.80380773923813</vol_abs_WMH>
- <vol_rel_WMH>0.00127699866138782</vol_rel_WMH>
- <surf_TSA>1872.28082827345</surf_TSA>
- <vol_TIV>1412.53690687332</vol_TIV>
- <vol_rel_CGW>[0.215660457096842 0.451402670470275 0.332936872432883 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.36607995331347 0.633495614622561]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.33374428749084 0.811756847062832 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.74522402114517 0.28188634642396 0.329228032824438;2.38865573595659 0.185848687591751 0.437908452696967;3.09726417203081 0.294427783518487 0.232863514478595]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.790688087913798 0.212806900604368 0.459923257301215;4.1907989107365 0.382202759283893 0.540076742698785]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00374375187644</vol_TIV>
- <vol_rel_CGW>[1.72306855418178 5.95694451275637 3.82932601352161 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.12769986613878</vol_rel_WMH>
- <surf_TSA>8.60851070782758</surf_TSA>
- <SQR>4.88894623755377</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 10813.4387561729 0.407415999373403]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00130932487081736 0.00118669820949435 0.0372160002589226]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[749.927599941508 428.98569293753 536.78694555172 1163.98639962118 904.428606728542 7750.94296531125]</SPMvols0>
- <SPMvols1>[641.909747339795 400.063325976005 325.363475376747 642.383892410524 770.174339951769 8035.77839204202]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[96.3088989257812 242.364395141602 343.228790283203]</T3th>
- <Tth>
- <T3th>[-4.9480299949646 -4.94803285598755 5.11292886734009 96.3088989257812 242.364395141602 343.228790283203 466.688720703125 820.860290527344]</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>[0.0214925836771727 0.0812770202755928 0.0917816609144211 0 0]</dtc>
- <ll>[0.0916186420857405 0 0.0916186420857405 0;0.215921243985876 0.0125964234570781 0.228517667442954 2686.162109375;0.215921243985876 0.0125964234570781 0.228517667442954 2686.162109375]</ll>
- <rmsdtc>[0.0454702861607075 0.114372350275517 0.128126308321953]</rmsdtc>
- <rmsgdt>[0.0320693552494049 0.0530108585953712 0.0651663914322853]</rmsgdt>
- <rmsdt>0.128126308321953</rmsdt>
- <dt>0.0917816609144211</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>[0.0096913781017065 0.0470604710280895 0.0492150150239468 0.0597478486597538 0.0675847381353378 0.0772967711091042]</dtc>
- <ll>[0.0907812338697847 0 0.0907812338697847 0;0.224840155677656 0.0174950988247863 0.242335254502442 8955.3037109375;0.220316642281913 0.0181660663397303 0.238482708621643 13074.3359375;0.19626145756822 0.0208787112041303 0.217140168772351 22512.9296875;0.177565612829429 0.0244013831470835 0.201966995976512 42686.6328125;0.177565612829429 0.0244013831470835 0.201966995976512 42686.6328125]</ll>
- <rmsdtc>[0.0120783466845751 0.0438569188117981 0.073342353105545 0.0954233258962631 0.123441897332668 0.131076365709305]</rmsdtc>
- <rmsgdt>[0.00338105810806155 0.0135296946391463 0.0311368089169264 0.0513053499162197 0.0727225244045258 0.0788816064596176]</rmsgdt>
- <rmsdt>0.131076365709305</rmsdt>
- <dt>0.0772967711091042</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026189/ses-2/sub-0026189_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 38s</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 4s</item>
- <item>Final scaling 4s</item>
- <item>27s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 58s</item>
- <item>SPM preprocessing 1 (estimate 2): 41s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 12s</item>
- <item>Update Segmentation 14s</item>
- <item>Update Skull-Stripping 31s</item>
- <item>Update probability maps 7s</item>
- <item>64s</item>
- <item>Global intensity correction: 12s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 25s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.15) 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 9s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.18) 14s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 4s</item>
- <item>45s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 26s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</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 | 0.0908 0.0000 0.0908 | 32.0000</item>
- <item>2 | 2.50 | 0.0882 0.0012 0.0894 | 29.4886</item>
- <item>3 | 2.50 | 0.0874 0.0018 0.0892 | 26.9772</item>
- <item>4 | 2.50 | 0.0870 0.0021 0.0891 | 24.6107</item>
- <item>5 | 2.50 | 0.0867 0.0022 0.0889 | 22.6548</item>
- <item>6 | 2.50 | 0.0864 0.0023 0.0887 | 20.6989</item>
- <item>7 | 2.50 | 0.0861 0.0024 0.0886 | 18.9688</item>
- <item>8 | 2.50 | 0.0858 0.0025 0.0884 | 17.4455</item>
- <item>9 | 2.50 | 0.0855 0.0026 0.0881 | 15.9223</item>
- <item>10 | 2.50 | 0.0852 0.0027 0.0879 | 14.6627</item>
- <item>11 | 2.50 | 0.0849 0.0028 0.0877 | 13.4764</item>
- <item>12 | 2.50 | 0.0845 0.0029 0.0875 | 12.3015</item>
- <item>13 | 2.50 | 0.0842 0.0030 0.0872 | 11.3776</item>
- <item>14 | 2.50 | 0.0839 0.0031 0.0870 | 10.4537</item>
- <item>15 | 2.25 | 0.0841 0.0032 0.0873 | 9.5920</item>
- <item>16 | 2.25 | 0.0807 0.0048 0.0856 | 8.8725</item>
- <item>17 | 2.25 | 0.0794 0.0054 0.0848 | 8.1530</item>
- <item>18 | 2.25 | 0.0785 0.0057 0.0842 | 7.5234</item>
- <item>19 | 2.25 | 0.0779 0.0058 0.0837 | 6.9630</item>
- <item>20 | 2.25 | 0.0773 0.0058 0.0832 | 6.4027</item>
- <item>21 | 2.25 | 0.0768 0.0059 0.0827 | 5.9447</item>
- <item>22 | 2.25 | 0.0763 0.0059 0.0822 | 5.5083</item>
- <item>23 | 2.25 | 0.0758 0.0058 0.0817 | 5.0803</item>
- <item>24 | 2.25 | 0.0754 0.0059 0.0812 | 4.7404</item>
- <item>25 | 2.25 | 0.0749 0.0058 0.0808 | 4.4005</item>
- <item>29 | 2.00 | 0.0767 0.0045 0.0813 | 3.3283</item>
- <item>30 | 2.00 | 0.0734 0.0061 0.0795 | 3.1221</item>
- <item>43 | 1.75 | 0.0722 0.0033 0.0756 | 1.5785</item>
- <item>44 | 1.75 | 0.0671 0.0060 0.0731 | 1.5194</item>
- <item>45 | 1.75 | 0.0654 0.0070 0.0724 | 1.4626</item>
- <item>57 | 1.50 | 0.0639 0.0051 0.0689 | 1.0900</item>
- <item>58 | 1.50 | 0.0604 0.0074 0.0678 | 1.0730</item>
- <item>59 | 1.50 | 0.0592 0.0081 0.0673 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 147s</item>
- <item>Prepare output 7s</item>
- <item>154s</item>
- <item>Jacobian determinant (RMS): 0.012 0.044 0.073 0.095 0.123 | 0.131076</item>
- <item>Template Matching: 0.091 0.225 0.220 0.196 0.178 | 0.177566</item>
- <item>Write result maps: 28s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 23s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 31s</item>
- <item>70s</item>
- <item>Create initial surface 59s</item>
- <item>Topology correction: 68s</item>
- <item>Surface refinement: 57s</item>
- <item>Reduction of surface collisions with optimization: 47s</item>
- <item>Spherical mapping with areal smoothing 65s</item>
- <item>Spherical registration 202s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 20s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 30s</item>
- <item>66s</item>
- <item>Create initial surface 54s</item>
- <item>Topology correction: 67s</item>
- <item>Surface refinement: 65s</item>
- <item>Reduction of surface collisions with optimization: 43s</item>
- <item>Spherical mapping with areal smoothing 73s</item>
- <item>Spherical registration 219s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3660 0.6334 mm</item>
- <item>Surface intensity / position RMSE: 0.0627 / 0.0609</item>
- <item>Euler number / defect number / defect size: 18.0 / 15.5 / 0.48%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/surf/lh.thickness.sub-0026189_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/surf/rh.thickness.sub-0026189_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/sub-0026189_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1227s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 24s</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 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 21s</item>
- <item>ROI estimation of 'julichbrain' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 27s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 53s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 79s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>327s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/report/catreport_sub-0026189_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 37 minute(s) and 57 second(s).</item>
- <item>Image Quality Rating (IQR): 75.37% (C)</item>
- <item>GM volume (GMV): 45.14% (637.62 / 1412.54 ml)</item>
- <item>GM thickness (GMT): 2.37 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3556103/ds/UM/sub-0026189/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|