123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.05906959832923 0.0503179930207189 -0.0151044045611434 -4.61597612412576;-0.0451881363117365 1.05618518779489 0.232967718102065 -34.6246068869457;0.0279471041130683 -0.260679089164934 1.17780027577696 3.5220184609929;0 0 0 1]</Affine>
- <Affine0>[1.05906959832923 0.0503179930207189 -0.0151044045611434 -4.61597612412576;-0.0451881363117365 1.05618518779489 0.232967718102065 -34.6246068869457;0.0279471041130683 -0.260679089164934 1.17780027577696 3.5220184609929;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[327.91450317213 410.202531762553 141.316758049966 234.70492323666 350.727226979303 30.5681361583165 99.0148660329691 371.011404875934 813.066034110652 571.226299753363 348.139630506862 280.954077777551 27.7106737911269]</mn>
- <vr>[1228.98817018947;262.842854826142;587.760142755221;2378.23968813892;20953.6426001008;239.175001402715;1950.35752351509;11123.5490168295;13610.4972092951;16266.5495884531;4296.17559284475;15273.8224350538;197.922149677361]</vr>
- <ll>-5.95614576339722</ll>
- <Affine_translation>[-4.61597612412576 -34.6246068869457 3.5220184609929]</Affine_translation>
- <Affine_rotation>[0.242686390738523 -0.0153603188350022 0.0477169615466231]</Affine_rotation>
- <Affine_scaling>[1.06040153828485 1.0890408632116 1.1993611756605]</Affine_scaling>
- <Affine_shearing>[-0.00153142162482093 0.00568465131602695 -0.0520409475674422]</Affine_shearing>
- <Affine0_translation>[-4.61597612412576 -34.6246068869457 3.5220184609929]</Affine0_translation>
- <Affine0_rotation>[0.242686390738523 -0.0153603188350022 0.0477169615466231]</Affine0_rotation>
- <Affine0_scaling>[1.06040153828485 1.0890408632116 1.1993611756605]</Affine0_scaling>
- <Affine0_shearing>[-0.00153142162482093 0.00568465131602695 -0.0520409475674422]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2</path>
- <file>sub-0025998_ses-2_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/sub-0025998_ses-2_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/sub-0025998_ses-2_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/mri/msub-0025998_ses-2_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/mri/p0sub-0025998_ses-2_run-1_T1w.nii</Fp0>
- <fnames>../XHCUMS/sub-0025998/ses-2/sub-0025998_ses-2_run-1_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
- <tol>0.0001</tol>
- <accstr>0.5</accstr>
- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
- <redspmres>0</redspmres>
- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
- </opts>
- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/var/lib/condor/execute/dir_3396818/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>0.9154351542986</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0642393082380295</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.068464383482933</SurfacePositionRMSE>
- <res_vx_vol>[1.00000000595636 0.999999988249227 0.999999988161106]</res_vx_vol>
- <res_vx_voli>[1.00000006523761 0.999999989132348 0.999999988669838]</res_vx_voli>
- <res_RMS>0.99999999412223</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[10.3800001144409 124.38500213623 309.289001464844 419.949005126953]</tissue_mn>
- <tissue_mnr>[0.0247172862291336 0.296190738677979 0.736491799354553 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[4.73344331700075 58.1425746613286 37.7711219962843 21.9771264294076]</tissue_std>
- <tissue_stdr>[0.0115571329370141 0.141960382461548 0.0922216325998306 0.0536591559648514]</tissue_stdr>
- <contrast>113.464546203613</contrast>
- <contrastr>0.270186483860016</contrastr>
- <res_ECR>0.242995083332062</res_ECR>
- <NCR>0.13387456536293</NCR>
- <ICR>0.445596188306808</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00000001191271 1.99999997649845 1.99999997632221]</res_vx_vol>
- <res_RMS>1.99999998824446</res_RMS>
- <res_ECR>2.13773012161255</res_ECR>
- <res_BB>1</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>4.03053617477417</contrastr>
- <NCR>2.25286483764648</NCR>
- <ICR>1.56497073173523</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.22885878857465</SurfaceDefectArea>
- <SurfaceDefectNumber>1.7</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.28478622436523</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.36928772926331</SurfacePositionRMSE>
- <SIQR>2.14723822623516</SIQR>
- <IQR>2.15188391609861</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>20231031-032141</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.9154351542986</SurfaceDefectArea>
- <SurfaceDefectNumber>14</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0642393082380295</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.068464383482933</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>0.9154351542986</defect_size>
- <vol_abs_CGW>[286.177306434658 591.183088189494 458.573506011417 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.574298063933354</vol_abs_WMH>
- <vol_rel_WMH>0.000429885089120152</vol_rel_WMH>
- <surf_TSA>1771.32525445715</surf_TSA>
- <vol_TIV>1335.93390063557</vol_TIV>
- <vol_rel_CGW>[0.214215169102685 0.44252420565736 0.343260625239955 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.31519228861506 0.628746224504734]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.2914834022522 0.798870208760199 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.70542348316418 0.270850732723943 0.330310141434642;2.34981524010655 0.183819286825945 0.437101400252285;3.04250377162345 0.29266793525166 0.232588458313073]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.774866912446394 0.210992050164558 0.477364901896306;4.13158618758789 0.394160959288658 0.522635098103694]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.09716441121645</vol_TIV>
- <vol_rel_CGW>[1.69711151405684 5.79748932574282 4.01473824066011 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04298850891202</vol_rel_WMH>
- <surf_TSA>8.56931997197507</surf_TSA>
- <SQR>4.77165615318148</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11534.3357966115 0.48723603354673]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0161505211144686 0.00168347836006433 0.216461420059204]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[712.886513035427 411.802751057237 527.462050152836 2412.89495090932 1817.51919979427 6415.97491927947]</SPMvols0>
- <SPMvols1>[583.525409428537 378.673710415684 337.230308631969 1264.46027795152 1684.59641368115 7286.38831360462]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[161.044799804688 317.150604248047 411.043395996094]</T3th>
- <Tth>
- <T3th>[-6.06578016281128 -6.0657811164856 9.05523872375488 161.044799804688 317.150604248047 411.043395996094 536.042724609375 1408.11633300781]</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>[0.0212255585938692 0.0919312760233879 0.104258567094803 0 0]</dtc>
- <ll>[0.0939937437377295 0 0.0939937437377295 0;0.210615838132128 0.0146697297388194 0.225285567870947 3128.29052734375;0.210615838132128 0.0146697297388194 0.225285567870947 3128.29052734375]</ll>
- <rmsdtc>[0.0484256930649281 0.125587686896324 0.140712007880211]</rmsdtc>
- <rmsgdt>[0.0349888801574707 0.0568834729492664 0.0698044672608376]</rmsgdt>
- <rmsdt>0.140712007880211</rmsdt>
- <dt>0.104258567094803</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>[0.00978845171630383 0.0458146221935749 0.0566459074616432 0.0659327805042267 0.0730530172586441 0.0828353017568588]</dtc>
- <ll>[0.0913614546941304 0 0.0913614546941304 0;0.223455631868132 0.0212328353937729 0.244688467261905 10868.5576171875;0.206588625033347 0.0215270665015138 0.22811569153486 15493.2880859375;0.185191169876432 0.0219845006495346 0.207175670525967 23705.271484375;0.167981247924233 0.0245111112151178 0.19249235913935 42878.5859375;0.167981247924233 0.0245111112151178 0.19249235913935 42878.5859375]</ll>
- <rmsdtc>[0.0119423400610685 0.0459936037659645 0.074163943529129 0.0989378243684769 0.123553030192852 0.130729719996452]</rmsdtc>
- <rmsgdt>[0.00353902764618397 0.0141517287120223 0.0311430245637894 0.0522461012005806 0.0712905898690224 0.0769830122590065]</rmsgdt>
- <rmsdt>0.130729719996452</rmsdt>
- <dt>0.0828353017568588</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025998/ses-2/sub-0025998_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 50s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 4s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 5s</item>
- <item>28s</item>
- <item>Correct center-of-mass 5s</item>
- <item>Affine registration 6s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 42s</item>
- <item>SPM preprocessing 1 (estimate 2): 36s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 10s</item>
- <item>Update Segmentation 12s</item>
- <item>Update Skull-Stripping 25s</item>
- <item>Update probability maps 6s</item>
- <item>54s</item>
- <item>Global intensity correction: 10s</item>
- <item>SANLM denoising after intensity normalization (medium): 12s</item>
- <item>Fast Optimized Shooting registration 21s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 2s</item>
- <item>Prepare partitions 1s</item>
- <item>Prepare segments (LASmod = 1.10) 8s</item>
- <item>Estimate local tissue thresholds (WM) 10s</item>
- <item>Estimate local tissue thresholds (GM) 15s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 26s</item>
- <item>65s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 4s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 5s</item>
- <item>Blood vessel detection 5s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.21) 11s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 2s</item>
- <item>Final corrections 3s</item>
- <item>34s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 20s</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) 2s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>7s</item>
- <item>Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):</item>
- <item>Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii"</item>
- <item>1 | 2.50 | 0.0914 0.0000 0.0914 | 32.0000</item>
- <item>2 | 2.50 | 0.0878 0.0015 0.0893 | 29.4886</item>
- <item>3 | 2.50 | 0.0867 0.0023 0.0890 | 26.9772</item>
- <item>4 | 2.50 | 0.0862 0.0026 0.0887 | 24.6107</item>
- <item>5 | 2.50 | 0.0857 0.0028 0.0885 | 22.6548</item>
- <item>6 | 2.50 | 0.0853 0.0029 0.0883 | 20.6989</item>
- <item>7 | 2.50 | 0.0849 0.0031 0.0880 | 18.9688</item>
- <item>8 | 2.50 | 0.0845 0.0032 0.0878 | 17.4455</item>
- <item>9 | 2.50 | 0.0841 0.0033 0.0875 | 15.9223</item>
- <item>10 | 2.50 | 0.0837 0.0035 0.0872 | 14.6627</item>
- <item>11 | 2.50 | 0.0832 0.0036 0.0868 | 13.4764</item>
- <item>12 | 2.50 | 0.0828 0.0037 0.0865 | 12.3015</item>
- <item>13 | 2.50 | 0.0823 0.0039 0.0862 | 11.3776</item>
- <item>14 | 2.50 | 0.0818 0.0040 0.0858 | 10.4537</item>
- <item>15 | 2.25 | 0.0821 0.0041 0.0862 | 9.5920</item>
- <item>16 | 2.25 | 0.0783 0.0060 0.0844 | 8.8725</item>
- <item>17 | 2.25 | 0.0769 0.0067 0.0835 | 8.1530</item>
- <item>18 | 2.25 | 0.0759 0.0069 0.0828 | 7.5234</item>
- <item>19 | 2.25 | 0.0751 0.0071 0.0822 | 6.9630</item>
- <item>20 | 2.25 | 0.0745 0.0071 0.0816 | 6.4027</item>
- <item>29 | 2.00 | 0.0758 0.0039 0.0798 | 3.3283</item>
- <item>30 | 2.00 | 0.0707 0.0063 0.0770 | 3.1221</item>
- <item>31 | 2.00 | 0.0689 0.0072 0.0760 | 2.9160</item>
- <item>43 | 1.75 | 0.0677 0.0041 0.0718 | 1.5785</item>
- <item>44 | 1.75 | 0.0632 0.0065 0.0697 | 1.5194</item>
- <item>45 | 1.75 | 0.0617 0.0073 0.0691 | 1.4626</item>
- <item>57 | 1.50 | 0.0603 0.0054 0.0657 | 1.0900</item>
- <item>58 | 1.50 | 0.0570 0.0075 0.0646 | 1.0730</item>
- <item>59 | 1.50 | 0.0560 0.0082 0.0642 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 106s</item>
- <item>Prepare output 6s</item>
- <item>112s</item>
- <item>Jacobian determinant (RMS): 0.012 0.046 0.074 0.099 0.124 | 0.130730</item>
- <item>Template Matching: 0.091 0.223 0.207 0.185 0.168 | 0.167981</item>
- <item>Write result maps: 21s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 20s</item>
- <item>CSF distance: 8s</item>
- <item>PBT2x thickness: 24s</item>
- <item>56s</item>
- <item>Create initial surface 43s</item>
- <item>Topology correction: 47s</item>
- <item>Surface refinement: 45s</item>
- <item>Reduction of surface collisions with optimization: 34s</item>
- <item>Spherical mapping with areal smoothing 46s</item>
- <item>Spherical registration 167s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 16s</item>
- <item>CSF distance: 8s</item>
- <item>PBT2x thickness: 23s</item>
- <item>50s</item>
- <item>Create initial surface 41s</item>
- <item>Topology correction: 46s</item>
- <item>Surface refinement: 50s</item>
- <item>Reduction of surface collisions with optimization: 34s</item>
- <item>Spherical mapping with areal smoothing 46s</item>
- <item>Spherical registration 177s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3153 0.6282 mm</item>
- <item>Surface intensity / position RMSE: 0.0642 / 0.0685</item>
- <item>Euler number / defect number / defect size: 30.0 / 14.0 / 0.92%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/surf/lh.thickness.sub-0025998_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/surf/rh.thickness.sub-0025998_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/sub-0025998_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 5s</item>
- <item>Surface and thickness estimation takes: 935s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 6s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 20s</item>
- <item>ROI estimation of 'lpba40' atlas 6s</item>
- <item>ROI estimation of 'hammers' atlas 14s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 5s</item>
- <item>ROI estimation of 'aal3' atlas 8s</item>
- <item>ROI estimation of 'mori' atlas 11s</item>
- <item>ROI estimation of 'anatomy3' atlas 16s</item>
- <item>ROI estimation of 'julichbrain' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 16s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 35s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 52s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 5s</item>
- <item>Write results 5s</item>
- <item>224s</item>
- <item>Quality check: 7s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/report/catreport_sub-0025998_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 29 minute(s) and 8 second(s).</item>
- <item>Image Quality Rating (IQR): 83.48% (B)</item>
- <item>GM volume (GMV): 44.25% (591.18 / 1335.93 ml)</item>
- <item>GM thickness (GMT): 2.32 0.63 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3396818/ds/XHCUMS/sub-0025998/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|