123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.05500949773057 -0.046299653513384 -0.0371784939022073 3.01240861759793;0.0588450770185749 0.926618630090191 0.285673232866639 -32.964203876718;0.0290031446746762 -0.301494381767891 1.0504820721449 1.33708104562268;0 0 0 1]</Affine>
- <Affine0>[1.05500949773057 -0.046299653513384 -0.0371784939022073 3.01240861759793;0.0588450770185749 0.926618630090191 0.285673232866639 -32.964203876718;0.0290031446746762 -0.301494381767891 1.0504820721449 1.33708104562268;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[179.835040105933 253.097590888872 114.896919903684 478.153422679565 93.5924795787347 30.3584035303618 51.7966646285079 183.724316855572 286.102233140331 153.576413071538 69.3625549801133 53.6703784831891 27.5226019646011]</mn>
- <vr>[952.95455752485;177.331775291901;1092.98445177301;47405.3557087225;492.827932087813;82.8087421149664;184.846081527322;3003.39310072591;9480.42800455827;1306.6865522111;513.094676984022;361.890058318687;75.3440400167377]</vr>
- <ll>-5.1241340637207</ll>
- <Affine_translation>[3.01240861759793 -32.964203876718 1.33708104562268]</Affine_translation>
- <Affine_rotation>[0.312509234962034 -0.0432807552426688 -0.0445519909699461]</Affine_rotation>
- <Affine_scaling>[1.05704728645035 0.975528679298906 1.08802182070426]</Affine_scaling>
- <Affine_shearing>[-0.00274212874452832 0.00720820708228675 -0.0528141005872792]</Affine_shearing>
- <Affine0_translation>[3.01240861759793 -32.964203876718 1.33708104562268]</Affine0_translation>
- <Affine0_rotation>[0.312509234962034 -0.0432807552426688 -0.0445519909699461]</Affine0_rotation>
- <Affine0_scaling>[1.05704728645035 0.975528679298906 1.08802182070426]</Affine0_scaling>
- <Affine0_shearing>[-0.00274212874452832 0.00720820708228675 -0.0528141005872792]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_50583/ds/sub-0278</path>
- <file>sub-0278_ses-01_T1w</file>
- <fname>/var/lib/condor/execute/dir_50583/ds/sub-0278/sub-0278_ses-01_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_50583/ds/sub-0278/sub-0278_ses-01_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_50583/ds/sub-0278/mri/msub-0278_ses-01_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_50583/ds/sub-0278/mri/p0sub-0278_ses-01_T1w.nii</Fp0>
- <fnames>..583/ds/sub-0278/sub-0278_ses-01_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>64</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>202</SurfaceEulerNumber>
- <SurfaceDefectArea>4.90393231944725</SurfaceDefectArea>
- <SurfaceDefectNumber>87</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0880219489336014</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.110326498746872</SurfacePositionRMSE>
- <res_vx_vol>[0.899992796565051 0.937499973494512 0.9375]</res_vx_vol>
- <res_vx_voli>[0.899992797033151 0.937499973494512 0.9375]</res_vx_voli>
- <res_RMS>0.925166558728966</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[12.5550003051758 72.8897094726562 156.987014770508 258.651153564453]</tissue_mn>
- <tissue_mnr>[0.0485402829945087 0.281807035207748 0.606944978237152 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[10.603435410441 40.0270792595222 33.6161890470392 21.0200971958071]</tissue_std>
- <tissue_stdr>[0.0430865548551083 0.162648141384125 0.136597782373428 0.0854141637682915]</tissue_stdr>
- <contrast>90.7120208740234</contrast>
- <contrastr>0.350711852312088</contrastr>
- <NCR>0.168403029441833</NCR>
- <ICR>0.528172671794891</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.7999855931301 1.87499994698902 1.875]</res_vx_vol>
- <res_RMS>1.85033311745793</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>2.82265543937683</contrastr>
- <NCR>2.74853610992432</NCR>
- <ICR>1.76977348327637</ICR>
- <SurfaceEulerNumber>10.5</SurfaceEulerNumber>
- <SurfaceDefectArea>2.22598307986181</SurfaceDefectArea>
- <SurfaceDefectNumber>5.35</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.76043891906738</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>2.20653009414673</SurfacePositionRMSE>
- <IQR>2.53347107565334</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>20220709-191014</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>202</SurfaceEulerNumber>
- <SurfaceDefectArea>4.90393231944725</SurfaceDefectArea>
- <SurfaceDefectNumber>87</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0880219489336014</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.110326498746872</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>202</EC_abs>
- <defect_size>4.90393231944725</defect_size>
- <vol_abs_CGW>[207.589355811248 789.837659990019 662.624384845396 0 0]</vol_abs_CGW>
- <vol_abs_WMH>1.93252560917767</vol_abs_WMH>
- <vol_rel_WMH>0.00116413600712898</vol_rel_WMH>
- <surf_TSA>2210.03682874288</surf_TSA>
- <vol_TIV>1660.05140064666</vol_TIV>
- <vol_rel_CGW>[0.125049956724462 0.475791086759327 0.399158956516211 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.36951243892131 0.685838519352374]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.39493227005005 0.816905265287551 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.65583006056381 0.302087216270152 0.287624151361496;2.3933698753532 0.201207808273256 0.41500048049474;3.10104182338257 0.283835300309 0.297375368143764]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.662017983711899 0.238854899331146 0.613658457550227;4.08907821063951 0.358997373616726 0.386341542449773]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.45234131732158</vol_TIV>
- <vol_rel_CGW>[0.5 6.39495486277527 5.01865942019056 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.1164136007129</vol_rel_WMH>
- <surf_TSA>8.62391967568326</surf_TSA>
- <SQR>5.31818958283467</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.138744354248047 1 1 10715.3121751562 0.467419655135462]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0468649193644524 0.0449112467467785 0.277909457683563]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1038.48721210079 605.210717064672 341.64252225199 506.25111435353 2080.63930044219 8735.92470689041]</SPMvols0>
- <SPMvols1>[859.726952295366 560.728419229074 179.002835982141 426.948061029221 1208.18234434635 9208.89541517139]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[80.3142013549805 171.970306396484 253.498001098633]</T3th>
- <Tth>
- <T3th>[0 0 16.0668811798096 80.3142013549805 171.970306396484 253.498001098633 340.089904785156 1085.27502441406]</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>[0.0133442608639598 0.0486460737884045 0.0524487122893333 0 0]</dtc>
- <ll>[0.0793758299218125 0 0.0793758299218125 0;0.202415896778633 0.00734043579284741 0.209756332571481 1565.33325195312;0.202415896778633 0.00734043579284741 0.209756332571481 1565.33325195312]</ll>
- <rmsdtc>[0.0308753773570061 0.0651919767260551 0.0750594735145569]</rmsdtc>
- <rmsgdt>[0.0225261561572552 0.0372894443571568 0.0472291223704815]</rmsgdt>
- <rmsdt>0.0750594735145569</rmsdt>
- <dt>0.0524487122893333</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>[0.00592799158766866 0.0240791384130716 0.0315504334867001 0.0416190400719643 0.0496748797595501 0.0558109804987907]</dtc>
- <ll>[0.0835563194108634 0 0.0835563194108634 0;0.224611431623932 0.0120125868055556 0.236624018429487 6148.94287109375;0.214051679699658 0.014886299843288 0.228937979542946 10713.8486328125;0.194239892624495 0.0185023323196744 0.21274222494417 19950.546875;0.177734836107978 0.0226000095642503 0.200334845672229 39535.39453125;0.177734836107978 0.0226000095642503 0.200334845672229 39535.39453125]</ll>
- <rmsdtc>[0.00704714609310031 0.0254864674061537 0.0438163243234158 0.0700400546193123 0.0991432964801788 0.107827104628086]</rmsdtc>
- <rmsgdt>[0.00276594515889883 0.0110548678785563 0.0268739219754934 0.049187246710062 0.071124903857708 0.0779687166213989]</rmsgdt>
- <rmsdt>0.107827104628086</rmsdt>
- <dt>0.0558109804987907</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_50583/ds/sub-0278/sub-0278_ses-01_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 196s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 10s</item>
- <item>Estimate background 11s</item>
- <item>Initial correction 27s</item>
- <item>Refine background 5s</item>
- <item>Final correction 13s</item>
- <item>Final scaling 9s</item>
- <item>85s</item>
- <item>Correct center-of-mass 6s</item>
- <item>Affine registration 28s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 121s</item>
- <item>SPM preprocessing 1 (estimate 2): 103s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 28s</item>
- <item>Update Segmentation 31s</item>
- <item>Update Skull-Stripping 67s</item>
- <item>Update probability maps 14s</item>
- <item>139s</item>
- <item>Global intensity correction: 26s</item>
- <item>SANLM denoising after intensity normalization (medium): 25s</item>
- <item>Fast Optimized Shooting registration 45s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 3s</item>
- <item>Prepare segments (LASmod = 1.12) 24s</item>
- <item>Estimate local tissue thresholds (WM) 32s</item>
- <item>Estimate local tissue thresholds (GM) 48s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 56s</item>
- <item>175s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 11s</item>
- <item>Major structures 6s</item>
- <item>Ventricle detection 26s</item>
- <item>Blood vessel detection 17s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 52s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 7s</item>
- <item>127s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 51s</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) 7s</item>
- <item>Level 1 cleanup (brain masking) 5s</item>
- <item>Level 2 cleanup (CSF correction) 3s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
- <item>19s</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 | 0.0836 0.0000 0.0836 | 32.0000</item>
- <item>2 | 2.50 | 0.0816 0.0009 0.0826 | 29.4886</item>
- <item>3 | 2.50 | 0.0811 0.0014 0.0825 | 26.9772</item>
- <item>4 | 2.50 | 0.0809 0.0015 0.0824 | 24.6107</item>
- <item>5 | 2.50 | 0.0807 0.0016 0.0823 | 22.6548</item>
- <item>6 | 2.50 | 0.0805 0.0017 0.0821 | 20.6989</item>
- <item>7 | 2.50 | 0.0803 0.0017 0.0820 | 18.9688</item>
- <item>8 | 2.50 | 0.0801 0.0018 0.0819 | 17.4455</item>
- <item>9 | 2.50 | 0.0799 0.0018 0.0817 | 15.9223</item>
- <item>10 | 2.50 | 0.0797 0.0019 0.0816 | 14.6627</item>
- <item>11 | 2.50 | 0.0795 0.0019 0.0814 | 13.4764</item>
- <item>12 | 2.50 | 0.0793 0.0019 0.0812 | 12.3015</item>
- <item>13 | 2.50 | 0.0791 0.0020 0.0811 | 11.3776</item>
- <item>14 | 2.50 | 0.0789 0.0020 0.0809 | 10.4537</item>
- <item>15 | 2.25 | 0.0795 0.0021 0.0816 | 9.5920</item>
- <item>16 | 2.25 | 0.0770 0.0033 0.0802 | 8.8725</item>
- <item>17 | 2.25 | 0.0760 0.0037 0.0797 | 8.1530</item>
- <item>18 | 2.25 | 0.0754 0.0039 0.0793 | 7.5234</item>
- <item>19 | 2.25 | 0.0749 0.0040 0.0789 | 6.9630</item>
- <item>29 | 2.00 | 0.0778 0.0020 0.0798 | 3.3283</item>
- <item>30 | 2.00 | 0.0731 0.0041 0.0772 | 3.1221</item>
- <item>31 | 2.00 | 0.0714 0.0050 0.0763 | 2.9160</item>
- <item>43 | 1.75 | 0.0710 0.0028 0.0738 | 1.5785</item>
- <item>44 | 1.75 | 0.0663 0.0053 0.0716 | 1.5194</item>
- <item>45 | 1.75 | 0.0647 0.0062 0.0709 | 1.4626</item>
- <item>57 | 1.50 | 0.0639 0.0044 0.0684 | 1.0900</item>
- <item>58 | 1.50 | 0.0604 0.0068 0.0672 | 1.0730</item>
- <item>59 | 1.50 | 0.0592 0.0075 0.0668 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 205s</item>
- <item>Prepare output 17s</item>
- <item>222s</item>
- <item>Jacobian determinant (RMS): 0.007 0.025 0.044 0.070 0.099 | 0.107827</item>
- <item>Template Matching: 0.084 0.225 0.214 0.194 0.178 | 0.177735</item>
- <item>Write result maps: 36s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 45s</item>
- <item>CSF distance: 23s</item>
- <item>PBT2x thickness: 66s</item>
- <item>142s</item>
- <item>Create initial surface 117s</item>
- <item>Topology correction: 154s</item>
- <item>Surface refinement: 136s</item>
- <item>Reduction of surface collisions with optimization: 90s</item>
- <item>Spherical mapping with areal smoothing 110s</item>
- <item>Spherical registration 336s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 42s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 65s</item>
- <item>136s</item>
- <item>Create initial surface 114s</item>
- <item>Topology correction: 138s</item>
- <item>Surface refinement: 132s</item>
- <item>Reduction of surface collisions with optimization: 96s</item>
- <item>Spherical mapping with areal smoothing 111s</item>
- <item>Spherical registration 344s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3698 0.6857 mm</item>
- <item>Surface intensity / position RMSE: 0.0880 / 0.1103</item>
- <item>Euler number / defect number / defect size: 202.0 / 87.0 / 4.90%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_50583/ds/sub-0278/surf/lh.thickness.sub-0278_ses-01_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_50583/ds/sub-0278/surf/rh.thickness.sub-0278_ses-01_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_50583/ds/sub-0278/sub-0278_ses-01_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 2287s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 15s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 46s</item>
- <item>ROI estimation of 'lpba40' atlas 13s</item>
- <item>ROI estimation of 'hammers' atlas 32s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 18s</item>
- <item>ROI estimation of 'mori' atlas 28s</item>
- <item>ROI estimation of 'anatomy3' atlas 38s</item>
- <item>ROI estimation of 'julichbrain' atlas 51s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 35s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 82s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 161s</item>
- <item>Write results 162s</item>
- <item>556s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_50583/ds/sub-0278/report/catreport_sub-0278_ses-01_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 73 minute(s) and 9 second(s).</item>
- <item>Image Quality Rating (IQR): 79.67% (C+)</item>
- <item>GM volume (GMV): 47.58% (789.84 / 1660.05 ml)</item>
- <item>GM thickness (GMT): 2.37 0.69 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_50583/ds/sub-0278/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_50583/ds/sub-0278/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_50583/ds/sub-0278/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|