123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[0.992458126257764 -0.0559981937729493 -0.0978129848834346 1.60709083619425;0.0855978584792429 0.987170644908589 0.26696741720268 9.47645760733927;0.0868595967845484 -0.266025447228258 1.09772942285841 -10.0983850221019;0 0 0 1]</Affine>
- <Affine0>[0.992458126257764 -0.0559981937729493 -0.0978129848834346 1.60709083619425;0.0855978584792429 0.987170644908589 0.26696741720268 9.47645760733927;0.0868595967845484 -0.266025447228258 1.09772942285841 -10.0983850221019;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[112.18300112407 161.97346268812 40.3360780678379 75.2693777899354 94.8667148658375 18.8754547721856 48.9100052768563 151.433275350241 274.011376649298 255.123058774024 119.519832874063 53.2231479492987 7.75141511458047]</mn>
- <vr>[360.042215225778;78.2932963835861;165.055127124503;251.923017372258;1051.36524393551;62.5605474299072;320.144147264998;1219.03376281633;3934.93856775888;4121.51232348121;550.798066569074;408.783618821829;9.30618155892495]</vr>
- <ll>-4.8901948928833</ll>
- <Affine_translation>[1.60709083619425 9.47645760733927 -10.0983850221019]</Affine_translation>
- <Affine_rotation>[0.257391375484549 -0.106190830595008 -0.06070916215257]</Affine_rotation>
- <Affine_scaling>[0.999922354638038 1.0239030110712 1.13353092394614]</Affine_scaling>
- <Affine_shearing>[0.00581787103768268 0.0211281634236235 -0.0220599138544406]</Affine_shearing>
- <Affine0_translation>[1.60709083619425 9.47645760733927 -10.0983850221019]</Affine0_translation>
- <Affine0_rotation>[0.257391375484549 -0.106190830595008 -0.06070916215257]</Affine0_rotation>
- <Affine0_scaling>[0.999922354638038 1.0239030110712 1.13353092394614]</Affine0_scaling>
- <Affine0_shearing>[0.00581787103768268 0.0211281634236235 -0.0220599138544406]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_7838/ds/sub-60</path>
- <file>sub-60_T1w</file>
- <fname>/var/lib/condor/execute/dir_7838/ds/sub-60/sub-60_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_7838/ds/sub-60/sub-60_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_7838/ds/sub-60/mri/msub-60_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_7838/ds/sub-60/mri/p0sub-60_T1w.nii</Fp0>
- <fnames>.._7838/ds/sub-60/sub-60_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>50</SurfaceEulerNumber>
- <SurfaceDefectArea>1.57638350482243</SurfaceDefectArea>
- <SurfaceDefectNumber>26.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.079657718539238</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.096246525645256</SurfacePositionRMSE>
- <res_vx_vol>[1.10000182021632 1.02734375 1.02734368271415]</res_vx_vol>
- <res_vx_voli>[1.10000182084032 1.02734375 1.02734368177816]</res_vx_voli>
- <res_RMS>1.05212075155468</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[4.63700008392334 30.0980224609375 100.640411376953 158.835006713867]</tissue_mn>
- <tissue_mnr>[0.0291938167065382 0.189492374658585 0.633616089820862 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[11.9881279425028 20.098947206294 17.7362185249224 10.8025301160496]</tissue_std>
- <tissue_stdr>[0.0777450278401375 0.130345061421394 0.115022368729115 0.0700562298297882]</tissue_stdr>
- <contrast>56.8395805358887</contrast>
- <contrastr>0.35785299539566</contrastr>
- <NCR>0.142802134156227</NCR>
- <ICR>0.382171601057053</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.20000364043264 2.0546875 2.0546873654283]</res_vx_vol>
- <res_RMS>2.10424150310936</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>2.7155385017395</contrastr>
- <NCR>2.38102388381958</NCR>
- <ICR>1.40766763687134</ICR>
- <SurfaceEulerNumber>3.44897959183673</SurfaceEulerNumber>
- <SurfaceDefectArea>1.39409587620561</SurfaceDefectArea>
- <SurfaceDefectNumber>2.325</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.5931544303894</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.92493057250977</SurfacePositionRMSE>
- <IQR>2.27147547682257</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <res_BB>brain next to the image boundary</res_BB>
- <tissue_mn>mean within the tissue classes</tissue_mn>
- <tissue_std>standard deviation within the tissue classes</tissue_std>
- <contrast>contrast between tissue classes</contrast>
- <contrastr>contrast between tissue classes</contrastr>
- <NCR>noise to contrast ratio</NCR>
- <ICR>inhomogeneity to contrast ratio</ICR>
- <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
- <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
- <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
- <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
- </qualitymeasures>
- <subjectmeasures>
- <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
- <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
- <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
- <surf_TSA>total surface area</surf_TSA>
- </subjectmeasures>
- </ratings_help>
- <software>
- <version_segment>1639</version_segment>
- <system>LINUX</system>
- <version_spm>7771</version_spm>
- <version_matlab>9.3</version_matlab>
- <version_cat>12.8.1</version_cat>
- <revision_cat>1980</revision_cat>
- <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
- <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
- <qamethod>cat12</qamethod>
- <date>20220703-111354</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>50</SurfaceEulerNumber>
- <SurfaceDefectArea>1.57638350482243</SurfaceDefectArea>
- <SurfaceDefectNumber>26.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.079657718539238</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.096246525645256</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>50</EC_abs>
- <defect_size>1.57638350482243</defect_size>
- <vol_abs_CGW>[226.850198485208 760.913299888635 595.777885940566 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.679273780924032</vol_abs_WMH>
- <vol_rel_WMH>0.000428958654098025</vol_rel_WMH>
- <surf_TSA>2183.27127704064</surf_TSA>
- <vol_TIV>1583.54138431441</vol_TIV>
- <vol_rel_CGW>[0.14325498577571 0.480513681186849 0.376231333037442 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.46671759990494 0.623891618364103]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.48662352561951 0.779753686458278 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.83530857829195 0.283406983128193 0.267217568356993;2.49309570022628 0.180214851600385 0.459757141965891;3.15397904049087 0.279803978093095 0.273025289677116]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.774198169654538 0.290476033686671 0.629654422224082;4.10567834212454 0.353789792287473 0.370345577775918]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.76180118660358</vol_TIV>
- <vol_rel_CGW>[0.5 6.47977157303967 4.60688457322992 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.0428958654098</vol_rel_WMH>
- <surf_TSA>8.62387077250149</surf_TSA>
- <SQR>5.34098581736725</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0.184763441337518 43 13 10575.7920485442 0.521678752039702]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.030946485882044 0.0332713474540183 0.0130452934769564]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[922.520862747326 539.410655185091 443.038320441763 1153.85186791627 1841.45408618372 9076.06741417644]</SPMvols0>
- <SPMvols1>[788.102212177532 503.737165051848 237.018876494369 711.452869866142 808.547466540554 9925.36741942583]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[39.9558982849121 106.591300964355 162.259506225586]</T3th>
- <Tth>
- <T3th>[0 0 5.40901136398315 39.9558982849121 106.591300964355 162.259506225586 223.411315917969 655.69580078125]</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>[0.0192806273698807 0.0680644437670708 0.0740263089537621 0 0]</dtc>
- <ll>[0.0804958946469213 0 0.0804958946469213 0;0.193554826715843 0.00881593081415916 0.202370757530002 1879.97961425781;0.193554826715843 0.00881593081415916 0.202370757530002 1879.97961425781]</ll>
- <rmsdtc>[0.0406320355832577 0.0866280272603035 0.095648854970932]</rmsdtc>
- <rmsgdt>[0.0288336127996445 0.0413077101111412 0.0507340393960476]</rmsgdt>
- <rmsdt>0.095648854970932</rmsdt>
- <dt>0.0740263089537621</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>[0.00847347639501095 0.0304138548672199 0.042587373405695 0.0509535856544971 0.0572340041399002 0.0634960755705833]</dtc>
- <ll>[0.0810166453068657 0 0.0810166453068657 0;0.216619261294261 0.0112296665140415 0.227848927808303 5748.185546875;0.197817777284525 0.0147147889103558 0.212532566194881 10590.41015625;0.178505661141159 0.017362940571813 0.195868601712972 18721.97265625;0.162507545646876 0.0204502303851767 0.182957776032053 35774.671875;0.162507545646876 0.0204502303851767 0.182957776032053 35774.671875]</ll>
- <rmsdtc>[0.00973797775804996 0.0345203280448914 0.0515750832855701 0.0743504092097282 0.0972997322678566 0.104731932282448]</rmsdtc>
- <rmsgdt>[0.00307649560272694 0.0118852341547608 0.026080172508955 0.0454622209072113 0.0634514689445496 0.0694693699479103]</rmsgdt>
- <rmsdt>0.104731932282448</rmsdt>
- <dt>0.0634960755705833</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./condor/execute/dir_7838/ds/sub-60/sub-60_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 112s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 31s</item>
- <item>Initial correction 9s</item>
- <item>Refine background 10s</item>
- <item>Final correction 10s</item>
- <item>Final scaling 23s</item>
- <item>95s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 10s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 66s</item>
- <item>SPM preprocessing 1 (estimate 2): 42s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 16s</item>
- <item>Update Segmentation 18s</item>
- <item>Update Skull-Stripping 39s</item>
- <item>Update probability maps 13s</item>
- <item>85s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 10s</item>
- <item>Fast Optimized Shooting registration 38s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 13s</item>
- <item>Estimate local tissue thresholds (WM) 36s</item>
- <item>Estimate local tissue thresholds (GM) 43s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 28s</item>
- <item>129s</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 9s</item>
- <item>WMH detection (WMHCstr=0.47 > WMHCstr'=0.00) 22s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>62s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 33s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.24):</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) 2s</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 | 0.0810 0.0000 0.0810 | 32.0000</item>
- <item>2 | 2.50 | 0.0791 0.0009 0.0800 | 29.4886</item>
- <item>3 | 2.50 | 0.0785 0.0014 0.0800 | 26.9772</item>
- <item>4 | 2.50 | 0.0782 0.0016 0.0799 | 24.6107</item>
- <item>5 | 2.50 | 0.0780 0.0017 0.0797 | 22.6548</item>
- <item>6 | 2.50 | 0.0778 0.0018 0.0796 | 20.6989</item>
- <item>7 | 2.50 | 0.0776 0.0019 0.0795 | 18.9688</item>
- <item>8 | 2.50 | 0.0774 0.0020 0.0793 | 17.4455</item>
- <item>9 | 2.50 | 0.0771 0.0020 0.0792 | 15.9223</item>
- <item>10 | 2.50 | 0.0769 0.0021 0.0790 | 14.6627</item>
- <item>11 | 2.50 | 0.0767 0.0022 0.0788 | 13.4764</item>
- <item>12 | 2.50 | 0.0764 0.0022 0.0786 | 12.3015</item>
- <item>13 | 2.50 | 0.0761 0.0023 0.0785 | 11.3776</item>
- <item>14 | 2.50 | 0.0759 0.0024 0.0783 | 10.4537</item>
- <item>15 | 2.25 | 0.0748 0.0024 0.0773 | 9.5920</item>
- <item>16 | 2.25 | 0.0722 0.0037 0.0759 | 8.8725</item>
- <item>29 | 2.00 | 0.0736 0.0017 0.0753 | 3.3283</item>
- <item>30 | 2.00 | 0.0679 0.0040 0.0718 | 3.1221</item>
- <item>31 | 2.00 | 0.0659 0.0049 0.0708 | 2.9160</item>
- <item>43 | 1.75 | 0.0651 0.0028 0.0679 | 1.5785</item>
- <item>44 | 1.75 | 0.0609 0.0050 0.0659 | 1.5194</item>
- <item>45 | 1.75 | 0.0595 0.0058 0.0653 | 1.4626</item>
- <item>57 | 1.50 | 0.0582 0.0042 0.0624 | 1.0900</item>
- <item>58 | 1.50 | 0.0552 0.0062 0.0613 | 1.0730</item>
- <item>59 | 1.50 | 0.0542 0.0068 0.0610 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 169s</item>
- <item>Prepare output 10s</item>
- <item>179s</item>
- <item>Jacobian determinant (RMS): 0.010 0.035 0.052 0.074 0.097 | 0.104732</item>
- <item>Template Matching: 0.081 0.217 0.198 0.179 0.163 | 0.162508</item>
- <item>Write result maps: 24s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 37s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 50s</item>
- <item>109s</item>
- <item>Create initial surface 94s</item>
- <item>Topology correction: 112s</item>
- <item>Surface refinement: 108s</item>
- <item>Reduction of surface collisions with optimization: 81s</item>
- <item>Spherical mapping with areal smoothing 95s</item>
- <item>Spherical registration 285s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 38s</item>
- <item>CSF distance: 15s</item>
- <item>PBT2x thickness: 44s</item>
- <item>103s</item>
- <item>Create initial surface 83s</item>
- <item>Topology correction: 99s</item>
- <item>Surface refinement: 118s</item>
- <item>Reduction of surface collisions with optimization: 79s</item>
- <item>Spherical mapping with areal smoothing 91s</item>
- <item>Spherical registration 271s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.4667 0.6234 mm</item>
- <item>Surface intensity / position RMSE: 0.0797 / 0.0962</item>
- <item>Euler number / defect number / defect size: 50.0 / 26.5 / 1.58%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_7838/ds/sub-60/surf/lh.thickness.sub-60_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_7838/ds/sub-60/surf/rh.thickness.sub-60_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_7838/ds/sub-60/sub-60_T1w.nii</item>
- <item>Surface ROI estimation: 8s</item>
- <item>Surface and thickness estimation takes: 1820s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 7s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 25s</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 10s</item>
- <item>ROI estimation of 'mori' atlas 15s</item>
- <item>ROI estimation of 'anatomy3' atlas 21s</item>
- <item>ROI estimation of 'julichbrain' atlas 29s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 21s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 69s</item>
- <item>Write results 70s</item>
- <item>291s</item>
- <item>Quality check: 4s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_7838/ds/sub-60/report/catreport_sub-60_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 51 minute(s) and 56 second(s).</item>
- <item>Image Quality Rating (IQR): 82.29% (B-)</item>
- <item>GM volume (GMV): 48.05% (760.91 / 1583.54 ml)</item>
- <item>GM thickness (GMT): 2.47 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_7838/ds/sub-60/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_7838/ds/sub-60/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_7838/ds/sub-60/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|