123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.0774839264083 -0.05941825014057 0.00323388085265878 -2.65417364072367;0.056137755737648 1.02805342559895 0.192120976021281 -22.0879994815763;-0.00262653370383751 -0.196693366900638 1.12963299939648 -74.7993699322112;0 0 0 1]</Affine>
- <Affine0>[1.0774839264083 -0.05941825014057 0.00323388085265878 -2.65417364072367;0.056137755737648 1.02805342559895 0.192120976021281 -22.0879994815763;-0.00262653370383751 -0.196693366900638 1.12963299939648 -74.7993699322112;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[289.633738395422 392.6616200631 110.460072044947 187.485562800149 65.9821348502057 23.4769236300344 40.3050360037673 259.787044977303 478.401885384697 351.892300023483 137.353288705203 31.5841910790067 18.6160707464497]</mn>
- <vr>[1425.44659333164;254.182624688071;774.05299298299;1008.17903954951;369.407826316305;56.813203144629;124.172733136527;2831.81693894337;4766.2443589639;7716.51571972063;2279.48980048526;112.253919726064;36.4435388530831]</vr>
- <ll>-5.4816632270813</ll>
- <Affine_translation>[-2.65417364072367 -22.0879994815763 -74.7993699322112]</Affine_translation>
- <Affine_rotation>[0.188622803047059 -0.00737467248089231 -0.0515865543223928]</Affine_rotation>
- <Affine_scaling>[1.07894854277987 1.04837198920667 1.14556604310001]</Affine_scaling>
- <Affine_shearing>[-0.00497622758792136 0.00970911867647421 -0.0225793490108174]</Affine_shearing>
- <Affine0_translation>[-2.65417364072367 -22.0879994815763 -74.7993699322112]</Affine0_translation>
- <Affine0_rotation>[0.188622803047059 -0.00737467248089231 -0.0515865543223928]</Affine0_rotation>
- <Affine0_scaling>[1.07894854277987 1.04837198920667 1.14556604310001]</Affine0_scaling>
- <Affine0_shearing>[-0.00497622758792136 0.00970911867647421 -0.0225793490108174]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1</path>
- <file>sub-0025291_ses-1_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/sub-0025291_ses-1_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/sub-0025291_ses-1_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/mri/msub-0025291_ses-1_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/mri/p0sub-0025291_ses-1_run-1_T1w.nii</Fp0>
- <fnames>../UPSM_1/sub-0025291/ses-1/sub-0025291_ses-1_run-1_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
- <tol>0.0001</tol>
- <accstr>0.5</accstr>
- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
- <redspmres>0</redspmres>
- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
- </opts>
- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/var/lib/condor/execute/dir_1959710/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>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.848081886314958</SurfaceDefectArea>
- <SurfaceDefectNumber>15</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0705883204936981</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0746440142393112</SurfacePositionRMSE>
- <res_vx_vol>[1.00007295608521 1 1.00007295608521]</res_vx_vol>
- <res_vx_voli>[1.00007295608521 1 1.00007295608521]</res_vx_voli>
- <res_RMS>1.00004863798151</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[12.9664993286133 92.8050003051758 270.385986328125 403.8330078125]</tissue_mn>
- <tissue_mnr>[0.0321085676550865 0.22981034219265 0.669548988342285 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[37.0728075803684 46.4871555681624 41.598999564566 25.7675495116683]</tissue_std>
- <tissue_stdr>[0.094847746193409 0.118933580815792 0.106427639722824 0.0659241676330566]</tissue_stdr>
- <contrast>137.873962402344</contrast>
- <contrastr>0.341413289308548</contrastr>
- <res_ECR>0.34484726190567</res_ECR>
- <NCR>0.138694107532501</NCR>
- <ICR>0.267248511314392</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.00014591217041 2 2.00014591217041]</res_vx_vol>
- <res_RMS>2.00009727596301</res_RMS>
- <res_ECR>2.65738391876221</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>2.96213388442993</contrastr>
- <NCR>2.32205152511597</NCR>
- <ICR>1.12264013290405</ICR>
- <SurfaceEulerNumber>1.91836734693878</SurfaceEulerNumber>
- <SurfaceDefectArea>1.21202047157874</SurfaceDefectArea>
- <SurfaceDefectNumber>1.75</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.41176640987396</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.49288034439087</SurfacePositionRMSE>
- <SIQR>2.4250338126278</SIQR>
- <IQR>2.2009537052238</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>20231030-234336</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>20</SurfaceEulerNumber>
- <SurfaceDefectArea>0.848081886314958</SurfaceDefectArea>
- <SurfaceDefectNumber>15</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0705883204936981</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0746440142393112</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>20</EC_abs>
- <defect_size>0.848081886314958</defect_size>
- <vol_abs_CGW>[223.805856346486 714.853490489247 481.487553088714 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.227401804511085</vol_abs_WMH>
- <vol_rel_WMH>0.000160125550760406</vol_rel_WMH>
- <surf_TSA>1956.68808397964</surf_TSA>
- <vol_TIV>1420.14689992445</vol_TIV>
- <vol_rel_CGW>[0.157593454844983 0.503365877521035 0.339040667633982 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.57845834386213 0.64308926109082]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.5854275226593 0.832358037411066 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.95288741819568 0.274494889264453 0.288715019917595;2.60958013798741 0.183829657581539 0.444395418642372;3.28490199233644 0.300847453989232 0.266889561440033]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.827456080827016 0.291047185916055 0.562036950201632;4.34427595516344 0.348230686682277 0.437963049798368]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.00966437917203</vol_TIV>
- <vol_rel_CGW>[0.680198542474546 6.89019176582319 3.93894877216203 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.01601255507604</vol_rel_WMH>
- <surf_TSA>8.6191666243853</surf_TSA>
- <SQR>5.64255541443412</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9373.01548738144 0.351064414290984]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00161540973931551 0.000960809295065701 0.303532630205154]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[841.581077602389 430.268456887585 309.357267384384 479.274351759669 1252.08071303906 6524.41844867054]</SPMvols0>
- <SPMvols1>[766.512980353906 405.399008921683 203.565977934856 401.274642486393 852.033684951067 6744.24118664027]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[115.894599914551 281.571594238281 393.005310058594]</T3th>
- <Tth>
- <T3th>[-6.23376989364624 -6.23376512527466 6.69866228103638 115.894599914551 281.571594238281 393.005310058594 531.560668945312 791.114318847656]</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>[0.0199849624186754 0.0698643773794174 0.0765065252780914 0 0]</dtc>
- <ll>[0.0810259894973615 0 0.0810259894973615 0;0.187490163301649 0.00932632059323974 0.196816483894889 1988.81921386719;0.187490163301649 0.00932632059323974 0.196816483894889 1988.81921386719]</ll>
- <rmsdtc>[0.0430945679545403 0.0911945030093193 0.100397132337093]</rmsdtc>
- <rmsgdt>[0.0307371597737074 0.0405633002519608 0.0496661476790905]</rmsgdt>
- <rmsdt>0.100397132337093</rmsdt>
- <dt>0.0765065252780914</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>[0.00960542075335979 0.0345628447830677 0.0481491461396217 0.0556123852729797 0.0604854412376881 0.0669196099042892]</dtc>
- <ll>[0.0825980502022106 0 0.0825980502022106 0;0.211378449328449 0.0136385731456044 0.225017022474054 6981.24462890625;0.190281624802699 0.015704456153121 0.20598608095582 11302.685546875;0.171835092397837 0.0170067065348539 0.18884179893269 18337.85546875;0.15914074732201 0.0177121109204374 0.176852858242447 30984.734375;0.15914074732201 0.0177121109204374 0.176852858242447 30984.734375]</ll>
- <rmsdtc>[0.0113968793302774 0.0404808856546879 0.0591263473033905 0.0800423696637154 0.0991520136594772 0.103429071605206]</rmsdtc>
- <rmsgdt>[0.0032197330147028 0.0121301701292396 0.025406040251255 0.0429823324084282 0.0591098628938198 0.0634003728628159]</rmsgdt>
- <rmsdt>0.103429071605206</rmsdt>
- <dt>0.0669196099042892</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025291/ses-1/sub-0025291_ses-1_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 32s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 3s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 3s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>21s</item>
- <item>Correct center-of-mass 2s</item>
- <item>Affine registration 5s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 45s</item>
- <item>SPM preprocessing 1 (estimate 2): 38s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 10s</item>
- <item>Update Segmentation 12s</item>
- <item>Update Skull-Stripping 24s</item>
- <item>Update probability maps 5s</item>
- <item>52s</item>
- <item>Global intensity correction: 9s</item>
- <item>SANLM denoising after intensity normalization (medium): 19s</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 = 1.00) 9s</item>
- <item>Estimate local tissue thresholds (WM) 11s</item>
- <item>Estimate local tissue thresholds (GM) 16s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 29s</item>
- <item>71s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 4s</item>
- <item>Major structures 2s</item>
- <item>Ventricle detection 7s</item>
- <item>Blood vessel detection 6s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 14s</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>40s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 23s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.06,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 3s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>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 | 0.0826 0.0000 0.0826 | 32.0000</item>
- <item>2 | 2.50 | 0.0796 0.0013 0.0809 | 29.4886</item>
- <item>3 | 2.50 | 0.0787 0.0019 0.0807 | 26.9772</item>
- <item>4 | 2.50 | 0.0783 0.0022 0.0805 | 24.6107</item>
- <item>5 | 2.50 | 0.0780 0.0023 0.0803 | 22.6548</item>
- <item>6 | 2.50 | 0.0777 0.0024 0.0801 | 20.6989</item>
- <item>7 | 2.50 | 0.0774 0.0025 0.0799 | 18.9688</item>
- <item>8 | 2.50 | 0.0771 0.0026 0.0797 | 17.4455</item>
- <item>9 | 2.50 | 0.0768 0.0027 0.0795 | 15.9223</item>
- <item>10 | 2.50 | 0.0765 0.0028 0.0792 | 14.6627</item>
- <item>11 | 2.50 | 0.0761 0.0028 0.0790 | 13.4764</item>
- <item>12 | 2.50 | 0.0758 0.0029 0.0787 | 12.3015</item>
- <item>13 | 2.50 | 0.0755 0.0030 0.0785 | 11.3776</item>
- <item>14 | 2.50 | 0.0752 0.0031 0.0782 | 10.4537</item>
- <item>15 | 2.25 | 0.0733 0.0031 0.0765 | 9.5920</item>
- <item>16 | 2.25 | 0.0705 0.0045 0.0750 | 8.8725</item>
- <item>29 | 2.00 | 0.0712 0.0021 0.0732 | 3.3283</item>
- <item>30 | 2.00 | 0.0653 0.0043 0.0697 | 3.1221</item>
- <item>31 | 2.00 | 0.0634 0.0052 0.0687 | 2.9160</item>
- <item>43 | 1.75 | 0.0623 0.0030 0.0653 | 1.5785</item>
- <item>44 | 1.75 | 0.0585 0.0050 0.0635 | 1.5194</item>
- <item>45 | 1.75 | 0.0573 0.0057 0.0629 | 1.4626</item>
- <item>57 | 1.50 | 0.0558 0.0041 0.0599 | 1.0900</item>
- <item>58 | 1.50 | 0.0530 0.0059 0.0590 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 96s</item>
- <item>Prepare output 7s</item>
- <item>103s</item>
- <item>Jacobian determinant (RMS): 0.011 0.040 0.059 0.080 0.099 | 0.103429</item>
- <item>Template Matching: 0.083 0.211 0.190 0.172 0.159 | 0.159141</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: 21s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 29s</item>
- <item>64s</item>
- <item>Create initial surface 53s</item>
- <item>Topology correction: 64s</item>
- <item>Surface refinement: 58s</item>
- <item>Reduction of surface collisions with optimization: 47s</item>
- <item>Spherical mapping with areal smoothing 58s</item>
- <item>Spherical registration 181s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 16s</item>
- <item>CSF distance: 10s</item>
- <item>PBT2x thickness: 28s</item>
- <item>57s</item>
- <item>Create initial surface 52s</item>
- <item>Topology correction: 63s</item>
- <item>Surface refinement: 51s</item>
- <item>Reduction of surface collisions with optimization: 46s</item>
- <item>Spherical mapping with areal smoothing 107s</item>
- <item>Spherical registration 187s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5785 0.6421 mm</item>
- <item>Surface intensity / position RMSE: 0.0706 / 0.0746</item>
- <item>Euler number / defect number / defect size: 20.0 / 15.0 / 0.85%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/surf/lh.thickness.sub-0025291_ses-1_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/surf/rh.thickness.sub-0025291_ses-1_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/sub-0025291_ses-1_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 6s</item>
- <item>Surface and thickness estimation takes: 1152s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 5s</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 13s</item>
- <item>ROI estimation of 'anatomy3' atlas 19s</item>
- <item>ROI estimation of 'julichbrain' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 52s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 76s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 8s</item>
- <item>294s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/report/catreport_sub-0025291_ses-1_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 34 minute(s) and 22 second(s).</item>
- <item>Image Quality Rating (IQR): 82.99% (B-)</item>
- <item>GM volume (GMV): 50.34% (714.85 / 1420.15 ml)</item>
- <item>GM thickness (GMT): 2.58 0.64 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1959710/ds/UPSM_1/sub-0025291/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|