123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.08267880557123 0.0415118405215536 -0.0841774366525153 -6.47825406683618;-0.00235457090071752 1.03218265722779 0.399205330898522 -20.580153433272;0.0996876787990874 -0.387008565415035 1.09028246114613 -33.2787980917597;0 0 0 1]</Affine>
- <Affine0>[1.08267880557123 0.0415118405215536 -0.0841774366525153 -6.47825406683618;-0.00235457090071752 1.03218265722779 0.399205330898522 -20.580153433272;0.0996876787990874 -0.387008565415035 1.09028246114613 -33.2787980917597;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[53106.0661137479 67597.277245152 22230.7453118845 34772.0643008546 12817.0371976946 3784.53888670606 7213.45474594602 33101.6120865021 63861.7541043494 44607.1333218484 20856.9377347363 26884.3973651947 3401.39506633082]</mn>
- <vr>[36767770.7412862;5064878.97116893;17733222.5396465;43614861.3549515;15484397.7709935;1967978.32661684;5300201.64833964;71767300.7512796;238313544.574704;51549249.7321083;49931255.7705584;72438492.9632005;3634460.82552287]</vr>
- <ll>-10.5735673904419</ll>
- <Affine_translation>[-6.47825406683618 -20.580153433272 -33.2787980917597]</Affine_translation>
- <Affine_rotation>[0.361933460267008 -0.0851335301678713 0.0344969483127098]</Affine_rotation>
- <Affine_scaling>[1.08726104194974 1.10312592704594 1.16395215532728]</Affine_scaling>
- <Affine_shearing>[0.00332758260857817 0.0140513747185073 -0.0110490683719532]</Affine_shearing>
- <Affine0_translation>[-6.47825406683618 -20.580153433272 -33.2787980917597]</Affine0_translation>
- <Affine0_rotation>[0.361933460267008 -0.0851335301678713 0.0344969483127098]</Affine0_rotation>
- <Affine0_scaling>[1.08726104194974 1.10312592704594 1.16395215532728]</Affine0_scaling>
- <Affine0_shearing>[0.00332758260857817 0.0140513747185073 -0.0110490683719532]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_11915/ds/sub-035</path>
- <file>sub-035_ses-t0_T1w</file>
- <fname>/var/lib/condor/execute/dir_11915/ds/sub-035/sub-035_ses-t0_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_11915/ds/sub-035/sub-035_ses-t0_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_11915/ds/sub-035/mri/msub-035_ses-t0_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_11915/ds/sub-035/mri/p0sub-035_ses-t0_T1w.nii</Fp0>
- <fnames>..1915/ds/sub-035/sub-035_ses-t0_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>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.535040847298987</SurfaceDefectArea>
- <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0593376792967319</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0602942854166031</SurfacePositionRMSE>
- <res_vx_vol>[0.999987337201291 0.999999997523243 0.999999968772942]</res_vx_vol>
- <res_vx_voli>[0.999987335858233 0.999999996276145 0.999999969891876]</res_vx_voli>
- <res_RMS>0.999995767850261</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[174.162002563477 21888.8203125 48935.43359375 69592.9375]</tissue_mn>
- <tissue_mnr>[0.00250258157029748 0.314526468515396 0.703166663646698 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[9350.14558113272 7670.76837017026 6987.78668426642 3809.13520704705]</tissue_std>
- <tissue_stdr>[0.134691894054413 0.110499911010265 0.100661337375641 0.0548718310892582]</tissue_stdr>
- <contrast>20709.33203125</contrast>
- <contrastr>0.297578066587448</contrastr>
- <NCR>0.130955338478088</NCR>
- <ICR>0.254484623670578</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[1.99997467440258 1.99999999504649 1.99999993754588]</res_vx_vol>
- <res_RMS>1.99999153570052</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>3.61966228485107</contrastr>
- <NCR>2.2109580039978</NCR>
- <ICR>1.09098374843597</ICR>
- <SurfaceEulerNumber>1.40816326530612</SurfaceEulerNumber>
- <SurfaceDefectArea>1.13376021182475</SurfaceDefectArea>
- <SurfaceDefectNumber>1.375</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.18675363063812</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.20588564872742</SurfacePositionRMSE>
- <IQR>2.12353560374783</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>20220713-013709</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>10</SurfaceEulerNumber>
- <SurfaceDefectArea>0.535040847298987</SurfaceDefectArea>
- <SurfaceDefectNumber>7.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0593376792967319</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0602942854166031</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>10</EC_abs>
- <defect_size>0.535040847298987</defect_size>
- <vol_abs_CGW>[294.865196938523 545.242590161713 468.886916599075 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.831663949223186</vol_abs_WMH>
- <vol_rel_WMH>0.000635345541790846</vol_rel_WMH>
- <surf_TSA>1680.03158204213</surf_TSA>
- <vol_TIV>1308.99470369931</vol_TIV>
- <vol_rel_CGW>[0.225260802129461 0.416535367653375 0.358203830217164 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.31180684800379 0.579203384206698]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.30728888511658 0.718801345218795 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.72235042615457 0.249759038692321 0.272488881273606;2.31745734875471 0.162677462913923 0.467358995180023;2.92519339727699 0.260175074654301 0.260152123546371]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.807733840886294 0.229082705399161 0.518253793710139;3.96501140958015 0.431250066491595 0.481746206289861]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.19478627333548</vol_TIV>
- <vol_rel_CGW>[1.89548854399176 5.33073576963676 4.28311476683125 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.06353455417908</vol_rel_WMH>
- <surf_TSA>8.47278164878071</surf_TSA>
- <SQR>4.44756193343315</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.566258198302469 12642 3883 4496.97790338569 0.396684026342394]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0 0 0.16806735098362]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[656.62827381053 427.030310844985 406.460019108141 502.861136170256 2942.28812862551 5966.40999066428]</SPMvols0>
- <SPMvols1>[579.2751815407 402.979984866712 277.624627626298 831.051376609559 2335.67074133864 5941.28555675655]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[23861.38671875 51719.12890625 67742.7890625]</T3th>
- <Tth>
- <T3th>[0 0 611.542785644531 23861.38671875 51719.12890625 67742.7890625 89683.4921875 126781.703125]</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>[0.0232058148831129 0.088877446949482 0.0993279963731766 0 0]</dtc>
- <ll>[0.0870250260748831 0 0.0870250260748831 0;0.197866561175251 0.0123860415290384 0.21025260270429 2641.29858398438;0.197866561175251 0.0123860415290384 0.21025260270429 2641.29858398438]</ll>
- <rmsdtc>[0.049008771777153 0.115826576948166 0.129271507263184]</rmsdtc>
- <rmsgdt>[0.0346985831856728 0.0534644275903702 0.0658428817987442]</rmsgdt>
- <rmsdt>0.129271507263184</rmsdt>
- <dt>0.0993279963731766</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>[0.0111437765881419 0.0429822988808155 0.0620075725018978 0.0708000957965851 0.0766767784953117 0.0876076966524124]</dtc>
- <ll>[0.0863594041758807 0 0.0863594041758807 0;0.223005021367521 0.0156443242521368 0.238649345619658 8007.9384765625;0.199937831035192 0.0186669882796869 0.218604819314879 13434.85546875;0.178397270122937 0.0203675164116753 0.198764786534613 21961.72265625;0.161033054077708 0.0230786910039026 0.18411174508161 40372.77734375;0.161033054077708 0.0230786910039026 0.18411174508161 40372.77734375]</ll>
- <rmsdtc>[0.0126361912116408 0.0482616983354092 0.0732587575912476 0.102538838982582 0.128481477499008 0.137431770563126]</rmsdtc>
- <rmsgdt>[0.00368599616922438 0.0148581257089972 0.0314641669392586 0.0541537441313267 0.0743210315704346 0.0809987410902977]</rmsgdt>
- <rmsdt>0.137431770563126</rmsdt>
- <dt>0.0876076966524124</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./dir_11915/ds/sub-035/sub-035_ses-t0_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 17s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 5s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 5s</item>
- <item>35s</item>
- <item>Correct center-of-mass 7s</item>
- <item>Affine registration 11s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 74s</item>
- <item>SPM preprocessing 1 (estimate 2): 50s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 38s</item>
- <item>Update probability maps 8s</item>
- <item>78s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 18s</item>
- <item>Fast Optimized Shooting registration 32s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.06) 13s</item>
- <item>Estimate local tissue thresholds (WM) 15s</item>
- <item>Estimate local tissue thresholds (GM) 20s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 29s</item>
- <item>86s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 12s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.18) 23s</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>61s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 32s</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) 4s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>11s</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 | 0.0864 0.0000 0.0864 | 32.0000</item>
- <item>2 | 2.50 | 0.0833 0.0013 0.0846 | 29.4886</item>
- <item>3 | 2.50 | 0.0824 0.0020 0.0844 | 26.9772</item>
- <item>4 | 2.50 | 0.0819 0.0023 0.0842 | 24.6107</item>
- <item>5 | 2.50 | 0.0816 0.0025 0.0840 | 22.6548</item>
- <item>6 | 2.50 | 0.0812 0.0026 0.0838 | 20.6989</item>
- <item>7 | 2.50 | 0.0809 0.0027 0.0836 | 18.9688</item>
- <item>8 | 2.50 | 0.0805 0.0028 0.0833 | 17.4455</item>
- <item>9 | 2.50 | 0.0802 0.0029 0.0831 | 15.9223</item>
- <item>10 | 2.50 | 0.0798 0.0031 0.0828 | 14.6627</item>
- <item>11 | 2.50 | 0.0794 0.0032 0.0825 | 13.4764</item>
- <item>12 | 2.50 | 0.0790 0.0032 0.0822 | 12.3015</item>
- <item>13 | 2.50 | 0.0786 0.0034 0.0819 | 11.3776</item>
- <item>14 | 2.50 | 0.0782 0.0035 0.0816 | 10.4537</item>
- <item>15 | 2.25 | 0.0776 0.0036 0.0811 | 9.5920</item>
- <item>16 | 2.25 | 0.0743 0.0052 0.0795 | 8.8725</item>
- <item>29 | 2.00 | 0.0755 0.0024 0.0779 | 3.3283</item>
- <item>30 | 2.00 | 0.0689 0.0051 0.0740 | 3.1221</item>
- <item>31 | 2.00 | 0.0666 0.0062 0.0729 | 2.9160</item>
- <item>43 | 1.75 | 0.0654 0.0036 0.0690 | 1.5785</item>
- <item>44 | 1.75 | 0.0609 0.0060 0.0669 | 1.5194</item>
- <item>45 | 1.75 | 0.0595 0.0068 0.0663 | 1.4626</item>
- <item>57 | 1.50 | 0.0579 0.0050 0.0628 | 1.0900</item>
- <item>58 | 1.50 | 0.0547 0.0070 0.0618 | 1.0730</item>
- <item>59 | 1.50 | 0.0537 0.0077 0.0614 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 167s</item>
- <item>Prepare output 10s</item>
- <item>176s</item>
- <item>Jacobian determinant (RMS): 0.013 0.048 0.073 0.103 0.128 | 0.137432</item>
- <item>Template Matching: 0.086 0.223 0.200 0.178 0.161 | 0.161033</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: 30s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 38s</item>
- <item>88s</item>
- <item>Create initial surface 71s</item>
- <item>Topology correction: 69s</item>
- <item>Surface refinement: 59s</item>
- <item>Reduction of surface collisions with optimization: 49s</item>
- <item>Spherical mapping with areal smoothing 65s</item>
- <item>Spherical registration 289s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 41s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 35s</item>
- <item>93s</item>
- <item>Create initial surface 69s</item>
- <item>Topology correction: 70s</item>
- <item>Surface refinement: 56s</item>
- <item>Reduction of surface collisions with optimization: 52s</item>
- <item>Spherical mapping with areal smoothing 67s</item>
- <item>Spherical registration 281s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.3118 0.5791 mm</item>
- <item>Surface intensity / position RMSE: 0.0593 / 0.0603</item>
- <item>Euler number / defect number / defect size: 10.0 / 7.5 / 0.54%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_11915/ds/sub-035/surf/lh.thickness.sub-035_ses-t0_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_11915/ds/sub-035/surf/rh.thickness.sub-035_ses-t0_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_11915/ds/sub-035/sub-035_ses-t0_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1458s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 26s</item>
- <item>ROI estimation of 'lpba40' atlas 7s</item>
- <item>ROI estimation of 'hammers' atlas 18s</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 16s</item>
- <item>ROI estimation of 'anatomy3' atlas 23s</item>
- <item>ROI estimation of 'julichbrain' atlas 31s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 23s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 51s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 85s</item>
- <item>Write results 86s</item>
- <item>318s</item>
- <item>Quality check: 6s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_11915/ds/sub-035/report/catreport_sub-035_ses-t0_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 44 minute(s) and 10 second(s).</item>
- <item>Image Quality Rating (IQR): 83.76% (B)</item>
- <item>GM volume (GMV): 41.65% (545.24 / 1308.99 ml)</item>
- <item>GM thickness (GMT): 2.31 0.58 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_11915/ds/sub-035/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_11915/ds/sub-035/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_11915/ds/sub-035/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|