123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[0.963029881555881 0.0064106873096105 0.00242674991386478 -1.9497833269276;-0.018619775083188 1.04354675912811 0.234097748738124 -32.6201621085265;0.00517953018886149 -0.179635616276337 1.10098880610519 -2.04234888170348;0 0 0 1]</Affine>
- <Affine0>[0.963029881555881 0.0064106873096105 0.00242674991386478 -1.9497833269276;-0.018619775083188 1.04354675912811 0.234097748738124 -32.6201621085265;0.00517953018886149 -0.179635616276337 1.10098880610519 -2.04234888170348;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[258.821733975072 333.2571513079 108.658148844331 184.501626522067 318.287118308289 28.6757194154306 97.131012560676 349.414560916554 579.771231809194 516.246612617755 278.630835382834 15.8036099009647 283.538838698425]</mn>
- <vr>[858.750926755214;171.751529013108;548.112830384366;1531.34689751612;13039.8522815132;203.923913967646;1964.35421908791;12427.4422980249;1450.3679542536;18157.1932574009;1028.37811293455;188.472490069697;2912.69852864332]</vr>
- <ll>-5.60239839553833</ll>
- <Affine_translation>[-1.9497833269276 -32.6201621085265 -2.04234888170348]</Affine_translation>
- <Affine_rotation>[0.170481053881016 -0.00202016198522685 0.0199640699996649]</Affine_rotation>
- <Affine_scaling>[0.963223793480341 1.05881204458403 1.1247370606403]</Affine_scaling>
- <Affine_shearing>[-0.0152913876197959 0.00396722322606805 0.0415553425505666]</Affine_shearing>
- <Affine0_translation>[-1.9497833269276 -32.6201621085265 -2.04234888170348]</Affine0_translation>
- <Affine0_rotation>[0.170481053881016 -0.00202016198522685 0.0199640699996649]</Affine0_rotation>
- <Affine0_scaling>[0.963223793480341 1.05881204458403 1.1247370606403]</Affine0_scaling>
- <Affine0_shearing>[-0.0152913876197959 0.00396722322606805 0.0415553425505666]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1</path>
- <file>sub-0025762_ses-1_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/sub-0025762_ses-1_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/sub-0025762_ses-1_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/mri/msub-0025762_ses-1_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/mri/p0sub-0025762_ses-1_run-1_T1w.nii</Fp0>
- <fnames>..s/SWU_4/sub-0025762/ses-1/sub-0025762_ses-1_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_2622078/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>30</SurfaceEulerNumber>
- <SurfaceDefectArea>1.79872887477408</SurfaceDefectArea>
- <SurfaceDefectNumber>14.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0773071274161339</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.100858516991138</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>208.911895751953</res_BB>
- <tissue_mn>[3.69099998474121 101.406997680664 236.369003295898 342.605987548828]</tissue_mn>
- <tissue_mnr>[0.0107733085751534 0.295987218618393 0.689915001392365 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[5.04328271282471 40.989700079636 32.989322356936 20.7312743470763]</tissue_std>
- <tissue_stdr>[0.0148806720972061 0.120943903923035 0.0973380506038666 0.0611695423722267]</tissue_stdr>
- <contrast>107.393974304199</contrast>
- <contrastr>0.313462048768997</contrastr>
- <res_ECR>0.334348678588867</res_ECR>
- <NCR>0.14639213681221</NCR>
- <ICR>0.347284525632858</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.60381984710693</res_ECR>
- <res_BB>10.5</res_BB>
- <tissue_mn>[8.62397575378418 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.38140249252319</contrastr>
- <NCR>2.43255996704102</NCR>
- <ICR>1.32114219665527</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.44968221869352</SurfaceDefectArea>
- <SurfaceDefectNumber>1.725</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.546142578125</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.01717042922974</SurfacePositionRMSE>
- <SIQR>2.42561621437453</SIQR>
- <IQR>2.28417374022701</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>20231031-020551</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>1.79872887477408</SurfaceDefectArea>
- <SurfaceDefectNumber>14.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0773071274161339</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.100858516991138</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>1.79872887477408</defect_size>
- <vol_abs_CGW>[298.955203921569 809.842650980392 578.361243137255 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.704682352941176</vol_abs_WMH>
- <vol_rel_WMH>0.000417673919288433</vol_rel_WMH>
- <surf_TSA>2154.68563402878</surf_TSA>
- <vol_TIV>1687.15909803922</vol_TIV>
- <vol_rel_CGW>[0.177194435467887 0.480003724557794 0.342801839974319 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.60859746418291 0.729941698046647]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.6487557888031 0.976850214764251 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.75393767837332 0.369338689144137 0.242987040312079;2.61237014939991 0.22423506084207 0.451257584459748;3.39202918782201 0.348713455047617 0.305755375228174]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.637973933288043 0.212316507137693 0.617224880382775;4.48760653115236 0.289598330015585 0.382775119617225]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.73189935468851</vol_TIV>
- <vol_rel_CGW>[1.03222764848935 6.47061286921326 4.00649856275716 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04176739192884</vol_rel_WMH>
- <surf_TSA>8.62378763936088</surf_TSA>
- <SQR>5.30560081696545</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.336 0.359875461309732]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00170624302700162 0.00146634492557496 0.344422161579132]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[962.7452 514.003933333333 544.164780392157 2695.4553372549 1001.92729411765 6729.64763921569]</SPMvols0>
- <SPMvols1>[826.984403921569 479.654160784314 336.464843137255 3181.49877254902 962.620474509804 5748.17246666667]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[118.849601745605 250.914794921875 333.136901855469]</T3th>
- <Tth>
- <T3th>[-5.21700000762939 -5.21699905395508 2.95359945297241 118.849601745605 250.914794921875 333.136901855469 440.280548095703 976.545776367188]</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>[0.0170818250626326 0.0616524033248425 0.0674399062991142 0 0]</dtc>
- <ll>[0.0825578705603335 0 0.0825578705603335 0;0.204296391408126 0.00946037022291827 0.213756761631044 2017.40502929688;0.204296391408126 0.00946037022291827 0.213756761631044 2017.40502929688]</ll>
- <rmsdtc>[0.0390412136912346 0.0824467241764069 0.0938134491443634]</rmsdtc>
- <rmsgdt>[0.0281817726790905 0.0434683561325073 0.054445918649435]</rmsgdt>
- <rmsdt>0.0938134491443634</rmsdt>
- <dt>0.0674399062991142</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>[0.00686287926509976 0.02470020391047 0.0348662659525871 0.0444462858140469 0.0519729219377041 0.0573476366698742]</dtc>
- <ll>[0.0827140321101084 0 0.0827140321101084 0;0.222768925518926 0.0115649095695971 0.234333835088523 5919.7880859375;0.206233535080699 0.0151508425093128 0.221384377590012 10904.2431640625;0.186079469048626 0.0183320113396713 0.204411480388297 19766.89453125;0.168648351704887 0.0218287221761417 0.190477073881029 38186.140625;0.168648351704887 0.0218287221761417 0.190477073881029 38186.140625]</ll>
- <rmsdtc>[0.00812279153615236 0.0279531441628933 0.0454957410693169 0.0707581788301468 0.09624844789505 0.102603904902935]</rmsdtc>
- <rmsgdt>[0.00277023180387914 0.0108969379216433 0.0260517373681068 0.0473224595189095 0.0673886388540268 0.0730637162923813]</rmsgdt>
- <rmsdt>0.102603904902935</rmsdt>
- <dt>0.0573476366698742</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025762/ses-1/sub-0025762_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 35s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 5s</item>
- <item>Initial correction 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>34s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 7s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 74s</item>
- <item>SPM preprocessing 1 (estimate 2): 55s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 37s</item>
- <item>Update probability maps 8s</item>
- <item>77s</item>
- <item>Global intensity correction: 13s</item>
- <item>SANLM denoising after intensity normalization (medium): 23s</item>
- <item>Fast Optimized Shooting registration 27s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 12s</item>
- <item>Estimate local tissue thresholds (WM) 16s</item>
- <item>Estimate local tissue thresholds (GM) 22s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 37s</item>
- <item>96s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 10s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.08) 19s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>55s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 29s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 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>9s</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 | 0.0827 0.0000 0.0827 | 32.0000</item>
- <item>2 | 2.50 | 0.0811 0.0009 0.0820 | 29.4886</item>
- <item>3 | 2.50 | 0.0806 0.0013 0.0819 | 26.9772</item>
- <item>4 | 2.50 | 0.0804 0.0015 0.0818 | 24.6107</item>
- <item>5 | 2.50 | 0.0802 0.0016 0.0817 | 22.6548</item>
- <item>6 | 2.50 | 0.0800 0.0016 0.0816 | 20.6989</item>
- <item>7 | 2.50 | 0.0798 0.0017 0.0815 | 18.9688</item>
- <item>8 | 2.50 | 0.0796 0.0018 0.0814 | 17.4455</item>
- <item>9 | 2.50 | 0.0794 0.0018 0.0812 | 15.9223</item>
- <item>10 | 2.50 | 0.0792 0.0019 0.0811 | 14.6627</item>
- <item>11 | 2.50 | 0.0790 0.0019 0.0810 | 13.4764</item>
- <item>12 | 2.50 | 0.0788 0.0020 0.0808 | 12.3015</item>
- <item>13 | 2.50 | 0.0786 0.0021 0.0806 | 11.3776</item>
- <item>14 | 2.50 | 0.0784 0.0021 0.0805 | 10.4537</item>
- <item>15 | 2.25 | 0.0780 0.0021 0.0801 | 9.5920</item>
- <item>16 | 2.25 | 0.0753 0.0034 0.0787 | 8.8725</item>
- <item>17 | 2.25 | 0.0743 0.0039 0.0781 | 8.1530</item>
- <item>29 | 2.00 | 0.0763 0.0017 0.0780 | 3.3283</item>
- <item>30 | 2.00 | 0.0706 0.0041 0.0747 | 3.1221</item>
- <item>31 | 2.00 | 0.0687 0.0051 0.0738 | 2.9160</item>
- <item>43 | 1.75 | 0.0680 0.0028 0.0708 | 1.5785</item>
- <item>44 | 1.75 | 0.0635 0.0053 0.0688 | 1.5194</item>
- <item>45 | 1.75 | 0.0620 0.0061 0.0681 | 1.4626</item>
- <item>57 | 1.50 | 0.0606 0.0044 0.0650 | 1.0900</item>
- <item>58 | 1.50 | 0.0573 0.0066 0.0639 | 1.0730</item>
- <item>59 | 1.50 | 0.0562 0.0073 0.0635 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 138s</item>
- <item>Prepare output 8s</item>
- <item>146s</item>
- <item>Jacobian determinant (RMS): 0.008 0.028 0.045 0.071 0.096 | 0.102604</item>
- <item>Template Matching: 0.083 0.223 0.206 0.186 0.169 | 0.168648</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: 27s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 39s</item>
- <item>86s</item>
- <item>Create initial surface 70s</item>
- <item>Topology correction: 87s</item>
- <item>Surface refinement: 77s</item>
- <item>Reduction of surface collisions with optimization: 67s</item>
- <item>Spherical mapping with areal smoothing 84s</item>
- <item>Spherical registration 233s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 36s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 41s</item>
- <item>97s</item>
- <item>Create initial surface 74s</item>
- <item>Topology correction: 85s</item>
- <item>Surface refinement: 81s</item>
- <item>Reduction of surface collisions with optimization: 71s</item>
- <item>Spherical mapping with areal smoothing 79s</item>
- <item>Spherical registration 250s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6086 0.7299 mm</item>
- <item>Surface intensity / position RMSE: 0.0773 / 0.1009</item>
- <item>Euler number / defect number / defect size: 30.0 / 14.5 / 1.80%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/surf/lh.thickness.sub-0025762_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/surf/rh.thickness.sub-0025762_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/sub-0025762_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1535s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 12s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 41s</item>
- <item>ROI estimation of 'lpba40' atlas 11s</item>
- <item>ROI estimation of 'hammers' atlas 32s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 17s</item>
- <item>ROI estimation of 'mori' atlas 25s</item>
- <item>ROI estimation of 'anatomy3' atlas 33s</item>
- <item>ROI estimation of 'julichbrain' atlas 45s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 61s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 88s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 8s</item>
- <item>Write results 9s</item>
- <item>434s</item>
- <item>Quality check: 10s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/report/catreport_sub-0025762_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 46 minute(s) and 40 second(s).</item>
- <item>Image Quality Rating (IQR): 82.16% (B-)</item>
- <item>GM volume (GMV): 48.00% (809.84 / 1687.16 ml)</item>
- <item>GM thickness (GMT): 2.61 0.73 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2622078/ds/SWU_4/sub-0025762/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|