123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.05132029124123 0.0711948634917888 0.0143691713178931 3.00931910534634;-0.0718498860374926 1.04422778705002 0.187922411792305 2.00746461722062;-0.000330007662828365 -0.206325163944297 1.12088263667389 -4.28671188780334;0 0 0 1]</Affine>
- <Affine0>[1.05132029124123 0.0711948634917888 0.0143691713178931 3.00931910534634;-0.0718498860374926 1.04422778705002 0.187922411792305 2.00746461722062;-0.000330007662828365 -0.206325163944297 1.12088263667389 -4.28671188780334;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[107.030611741955 156.279002136598 59.3582520861364 119.188546821321 50.1345272722279 11.047406801131 23.1600663982924 123.206470982182 237.724516309787 192.605960150013 124.946300789666 118.897656483748 12.3414665133796]</mn>
- <vr>[309.592514522784;52.4614685811049;573.71972059275;1304.47585742624;315.876014683843;18.9615834260633;65.9475357442723;488.866191393054;3057.90326931056;3129.77952663594;1415.36078291051;5129.57692466694;43.7865170802495]</vr>
- <ll>-4.8398585319519</ll>
- <Affine_translation>[3.00931910534634 2.00746461722062 -4.28671188780334]</Affine_translation>
- <Affine_rotation>[0.194171050512647 0.0134940918276353 0.0668916168737422]</Affine_rotation>
- <Affine_scaling>[1.05377268412319 1.06679447037619 1.13616965611008]</Affine_scaling>
- <Affine_shearing>[-9.99192241733635e-05 0.00111172249228234 -0.0298838731348679]</Affine_shearing>
- <Affine0_translation>[3.00931910534634 2.00746461722062 -4.28671188780334]</Affine0_translation>
- <Affine0_rotation>[0.194171050512647 0.0134940918276353 0.0668916168737422]</Affine0_rotation>
- <Affine0_scaling>[1.05377268412319 1.06679447037619 1.13616965611008]</Affine0_scaling>
- <Affine0_shearing>[-9.99192241733635e-05 0.00111172249228234 -0.0298838731348679]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_31527/ds/sub-102</path>
- <file>sub-102_T1w</file>
- <fname>/var/lib/condor/execute/dir_31527/ds/sub-102/sub-102_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_31527/ds/sub-102/sub-102_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_31527/ds/sub-102/mri/msub-102_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_31527/ds/sub-102/mri/p0sub-102_T1w.nii</Fp0>
- <fnames>..1527/ds/sub-102/sub-102_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
- <tol>0.0001</tol>
- <accstr>0.5</accstr>
- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
- <redspmres>0</redspmres>
- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
- </opts>
- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>32</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- </atlas>
- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
- <new_release>0</new_release>
- <lazy>0</lazy>
- <affmod>0</affmod>
- <regmethod>
- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
- </shooting>
- </regmethod>
- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
- <darteltpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>34</SurfaceEulerNumber>
- <SurfaceDefectArea>1.46704024848597</SurfaceDefectArea>
- <SurfaceDefectNumber>20</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0730003863573074</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0829935967922211</SurfacePositionRMSE>
- <res_vx_vol>[1.09999847412109 1 1]</res_vx_vol>
- <res_vx_voli>[1.09999847412109 1 1]</res_vx_voli>
- <res_RMS>1.03440750240073</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[4.83900022506714 78.9036636352539 98.2738952636719 154.316833496094]</tissue_mn>
- <tissue_mnr>[0.0313575640320778 0.511309504508972 0.636831939220428 0.999999940395355]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[28.8311133598457 32.8162457839746 17.0519304332183 9.95202489191033]</tissue_std>
- <tissue_stdr>[0.192878842353821 0.219539195299149 0.114076644182205 0.066578596830368]</tissue_stdr>
- <contrast>55.299186706543</contrast>
- <contrastr>0.358348369598389</contrastr>
- <NCR>0.147835582494736</NCR>
- <ICR>0.393942832946777</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.19999694824219 2 2]</res_vx_vol>
- <res_RMS>2.06881500480146</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.70810770988464</contrastr>
- <NCR>2.45328140258789</NCR>
- <ICR>1.4368622303009</ICR>
- <SurfaceEulerNumber>2.63265306122449</SurfaceEulerNumber>
- <SurfaceDefectArea>1.36676006212149</SurfaceDefectArea>
- <SurfaceDefectNumber>2</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.4600076675415</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.65987193584442</SurfacePositionRMSE>
- <IQR>2.31462677632774</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <res_BB>brain next to the image boundary</res_BB>
- <tissue_mn>mean within the tissue classes</tissue_mn>
- <tissue_std>standard deviation within the tissue classes</tissue_std>
- <contrast>contrast between tissue classes</contrast>
- <contrastr>contrast between tissue classes</contrastr>
- <NCR>noise to contrast ratio</NCR>
- <ICR>inhomogeneity to contrast ratio</ICR>
- <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
- <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
- <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
- <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
- </qualitymeasures>
- <subjectmeasures>
- <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
- <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
- <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
- <surf_TSA>total surface area</surf_TSA>
- </subjectmeasures>
- </ratings_help>
- <software>
- <version_segment>1639</version_segment>
- <system>LINUX</system>
- <version_spm>7771</version_spm>
- <version_matlab>9.3</version_matlab>
- <version_cat>12.8.1</version_cat>
- <revision_cat>1980</revision_cat>
- <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
- <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
- <qamethod>cat12</qamethod>
- <date>20220703-105530</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>34</SurfaceEulerNumber>
- <SurfaceDefectArea>1.46704024848597</SurfaceDefectArea>
- <SurfaceDefectNumber>20</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0730003863573074</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0829935967922211</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>34</EC_abs>
- <defect_size>1.46704024848597</defect_size>
- <vol_abs_CGW>[279.529321658594 681.450379029906 498.434267805331 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.735303685895134</vol_abs_WMH>
- <vol_rel_WMH>0.000503834896587974</vol_rel_WMH>
- <surf_TSA>2009.38884748302</surf_TSA>
- <vol_TIV>1459.41396849383</vol_TIV>
- <vol_rel_CGW>[0.19153532013064 0.466934258367547 0.341530421501813 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.51862452333452 0.611160768637203]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.52062606811523 0.745655865116092 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95016311097067 0.256493916094415 0.30473468896643;2.55775915169739 0.1741150861365 0.438605462639875;3.20729841487244 0.271750876406123 0.256659848393695]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.88379101149303 0.329480030162865 0.58455497382199;4.13183962505071 0.333945986227975 0.41544502617801]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.08364053762284</vol_TIV>
- <vol_rel_CGW>[1.28978664027731 6.23588826091141 3.98366417927106 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0503834896588</vol_rel_WMH>
- <surf_TSA>8.62177978525056</surf_TSA>
- <SQR>5.11696625641947</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.119772992176045 9 3 10819.0987921295 0.47719301562095]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0391949936747551 0.0407667011022568 0.0817375406622887]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[889.445699917932 483.810077111098 584.708239501684 2961.68531832174 2032.95116270728 6176.3397833807]</SPMvols0>
- <SPMvols1>[700.319334424187 475.827271713975 266.160397458394 2708.45468253548 1812.8763530853 6327.7621223526]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[39.9169006347656 102.432403564453 155.819702148438]</T3th>
- <Tth>
- <T3th>[0 4.38185119628906 5.97105312347412 39.9169006347656 102.432403564453 155.819702148438 213.771102905273 605.501892089844]</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>[0.0171221662312746 0.0653883516788483 0.0717590600252151 0 0]</dtc>
- <ll>[0.0862317644342893 0 0.0862317644342893 0;0.211342654737676 0.00981703411345007 0.221159688851126 2093.462890625;0.211342654737676 0.00981703411345007 0.221159688851126 2093.462890625]</ll>
- <rmsdtc>[0.0394476018846035 0.0876588374376297 0.100099734961987]</rmsdtc>
- <rmsgdt>[0.0287005510181189 0.0456562004983425 0.0580701529979706]</rmsgdt>
- <rmsdt>0.100099734961987</rmsdt>
- <dt>0.0717590600252151</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>[0.00975510198622942 0.0547905527055264 0.0575270690023899 0.0698275938630104 0.0791114717721939 0.108662977814674]</dtc>
- <ll>[0.0952366894029126 0 0.0952366894029126 0;0.223173489010989 0.0289540388431013 0.25212752785409 14820.8486328125;0.216281890360311 0.0281795986623816 0.244461489022692 20281.1953125;0.187347832341932 0.029020970589981 0.216368802931913 31292.5;0.166610133860919 0.0332053255903754 0.199815459451294 58087.8359375;0.166610133860919 0.0332053255903754 0.199815459451294 58087.8359375]</ll>
- <rmsdtc>[0.0126624424010515 0.0566890873014927 0.1225920394063 0.190439879894257 1.6268447637558 0.377339661121368]</rmsdtc>
- <rmsgdt>[0.00461173476651311 0.023442517966032 0.0604386366903782 0.102539837360382 2.0431764125824 0.234630927443504]</rmsgdt>
- <rmsdt>0.377339661121368</rmsdt>
- <dt>0.108662977814674</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./execute/dir_31527/ds/sub-102/sub-102_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 98s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 10s</item>
- <item>Initial correction 8s</item>
- <item>Refine background 4s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 9s</item>
- <item>50s</item>
- <item>Correct center-of-mass 12s</item>
- <item>Affine registration 8s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 6s</item>
- <item>Use initial fine affine registration. 7s</item>
- <item>Use previous fine affine registration. 51s</item>
- <item>SPM preprocessing 1 (estimate 2): 48s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 18s</item>
- <item>Update Skull-Stripping 38s</item>
- <item>Update probability maps 9s</item>
- <item>81s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 13s</item>
- <item>Fast Optimized Shooting registration 32s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.01) 13s</item>
- <item>Estimate local tissue thresholds (WM) 18s</item>
- <item>Estimate local tissue thresholds (GM) 24s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 27s</item>
- <item>90s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 13s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.48 > WMHCstr'=0.00) 27s</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>66s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 28s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.24):</item>
- <item>Level 1 cleanup (ROI estimation) 4s</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>10s</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 | 0.0952 0.0000 0.0952 | 32.0000</item>
- <item>2 | 2.50 | 0.0913 0.0015 0.0928 | 29.4886</item>
- <item>3 | 2.50 | 0.0901 0.0024 0.0925 | 26.9772</item>
- <item>4 | 2.50 | 0.0894 0.0028 0.0922 | 24.6107</item>
- <item>5 | 2.50 | 0.0889 0.0031 0.0919 | 22.6548</item>
- <item>6 | 2.50 | 0.0884 0.0033 0.0916 | 20.6989</item>
- <item>7 | 2.50 | 0.0879 0.0034 0.0913 | 18.9688</item>
- <item>8 | 2.50 | 0.0874 0.0036 0.0910 | 17.4455</item>
- <item>9 | 2.50 | 0.0869 0.0038 0.0907 | 15.9223</item>
- <item>10 | 2.50 | 0.0864 0.0040 0.0904 | 14.6627</item>
- <item>11 | 2.50 | 0.0858 0.0042 0.0900 | 13.4764</item>
- <item>12 | 2.50 | 0.0853 0.0043 0.0896 | 12.3015</item>
- <item>13 | 2.50 | 0.0847 0.0045 0.0892 | 11.3776</item>
- <item>14 | 2.50 | 0.0841 0.0047 0.0888 | 10.4537</item>
- <item>15 | 2.25 | 0.0889 0.0048 0.0937 | 9.5920</item>
- <item>16 | 2.25 | 0.0844 0.0073 0.0917 | 8.8725</item>
- <item>17 | 2.25 | 0.0825 0.0082 0.0906 | 8.1530</item>
- <item>18 | 2.25 | 0.0811 0.0086 0.0897 | 7.5234</item>
- <item>19 | 2.25 | 0.0800 0.0089 0.0889 | 6.9630</item>
- <item>20 | 2.25 | 0.0790 0.0091 0.0881 | 6.4027</item>
- <item>21 | 2.25 | 0.0780 0.0093 0.0873 | 5.9447</item>
- <item>22 | 2.25 | 0.0771 0.0094 0.0865 | 5.5083</item>
- <item>23 | 2.25 | 0.0762 0.0094 0.0857 | 5.0803</item>
- <item>24 | 2.25 | 0.0752 0.0096 0.0848 | 4.7404</item>
- <item>25 | 2.25 | 0.0744 0.0097 0.0840 | 4.4005</item>
- <item>29 | 2.00 | 0.0759 0.0077 0.0836 | 3.3283</item>
- <item>30 | 2.00 | 0.0721 0.0094 0.0815 | 3.1221</item>
- <item>43 | 1.75 | 0.0710 0.0052 0.0762 | 1.5785</item>
- <item>44 | 1.75 | 0.0648 0.0084 0.0732 | 1.5194</item>
- <item>45 | 1.75 | 0.0624 0.0097 0.0721 | 1.4626</item>
- <item>57 | 1.50 | 0.0613 0.0074 0.0687 | 1.0900</item>
- <item>Problem with Shooting (dets: 0.00174764 .. 2.43709)</item>
- <item>58 | 1.50 | 0.0571 0.0102 0.0673 | 1.0730</item>
- <item>59 | 1.50 | 0.0555 0.0111 0.0666 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 179s</item>
- <item>Prepare output 10s</item>
- <item>188s</item>
- <item>Jacobian determinant (RMS): 0.013 0.057 0.123 0.190 1.627 | 0.377340</item>
- <item>Template Matching: 0.095 0.223 0.216 0.187 0.167 | 0.166610</item>
- <item>Write result maps: 23s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 33s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 47s</item>
- <item>103s</item>
- <item>Create initial surface 87s</item>
- <item>Topology correction: 95s</item>
- <item>Surface refinement: 88s</item>
- <item>Reduction of surface collisions with optimization: 79s</item>
- <item>Spherical mapping with areal smoothing 87s</item>
- <item>Spherical registration 292s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 35s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 44s</item>
- <item>100s</item>
- <item>Create initial surface 83s</item>
- <item>Topology correction: 93s</item>
- <item>Surface refinement: 79s</item>
- <item>Reduction of surface collisions with optimization: 73s</item>
- <item>Spherical mapping with areal smoothing 82s</item>
- <item>Spherical registration 283s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5187 0.6105 mm</item>
- <item>Surface intensity / position RMSE: 0.0730 / 0.0830</item>
- <item>Euler number / defect number / defect size: 34.0 / 20.0 / 1.47%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_31527/ds/sub-102/surf/lh.thickness.sub-102_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_31527/ds/sub-102/surf/rh.thickness.sub-102_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_31527/ds/sub-102/sub-102_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1717s</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 7s</item>
- <item>ROI estimation of 'hammers' atlas 17s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 6s</item>
- <item>ROI estimation of 'aal3' atlas 11s</item>
- <item>ROI estimation of 'mori' atlas 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 22s</item>
- <item>ROI estimation of 'julichbrain' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 12s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 47s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 71s</item>
- <item>Write results 71s</item>
- <item>292s</item>
- <item>Quality check: 4s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_31527/ds/sub-102/report/catreport_sub-102_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 48 minute(s) and 36 second(s).</item>
- <item>Image Quality Rating (IQR): 81.85% (B-)</item>
- <item>GM volume (GMV): 46.69% (681.45 / 1459.41 ml)</item>
- <item>GM thickness (GMT): 2.52 0.61 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_31527/ds/sub-102/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_31527/ds/sub-102/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_31527/ds/sub-102/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|