123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.07175002172774 -0.0308211534116094 -0.0289092635872191 5.59486467759655;0.0411920162242312 1.0070135548421 0.125637623922938 -10.0787350753918;0.0248894078263078 -0.129432847736869 1.11060639077075 -53.0243797892852;0 0 0 1]</Affine>
- <Affine0>[1.07175002172774 -0.0308211534116094 -0.0289092635872191 5.59486467759655;0.0411920162242312 1.0070135548421 0.125637623922938 -10.0787350753918;0.0248894078263078 -0.129432847736869 1.11060639077075 -53.0243797892852;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[333.079978126019 464.751171652699 109.468991112609 210.003024333451 145.73200986276 44.280925469385 78.7606506360196 249.885104295571 387.141056348318 285.359556779861 128.150466373347 47.6381693999296 26.7524825695237]</mn>
- <vr>[2098.58698284476;434.275856368448;990.09388921935;2217.39660640003;1695.98133144072;195.857251684589;531.630203359723;4689.6189219745;16141.4201610393;5189.3610461104;1638.75103747078;240.524120216644;74.8693035915403]</vr>
- <ll>-5.64831590652466</ll>
- <Affine_translation>[5.59486467759655 -10.0787350753918 -53.0243797892852]</Affine_translation>
- <Affine_rotation>[0.126983463996712 -0.0278963464017166 -0.035155677370498]</Affine_rotation>
- <Affine_scaling>[1.07283007689754 1.01575359645714 1.11794685738062]</Affine_scaling>
- <Affine_shearing>[0.00454126994337283 0.00159353199913654 -0.0158443274132379]</Affine_shearing>
- <Affine0_translation>[5.59486467759655 -10.0787350753918 -53.0243797892852]</Affine0_translation>
- <Affine0_rotation>[0.126983463996712 -0.0278963464017166 -0.035155677370498]</Affine0_rotation>
- <Affine0_scaling>[1.07283007689754 1.01575359645714 1.11794685738062]</Affine0_scaling>
- <Affine0_shearing>[0.00454126994337283 0.00159353199913654 -0.0158443274132379]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2</path>
- <file>sub-0025238_ses-2_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/sub-0025238_ses-2_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/sub-0025238_ses-2_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/mri/msub-0025238_ses-2_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/mri/p0sub-0025238_ses-2_run-1_T1w.nii</Fp0>
- <fnames>../UPSM_1/sub-0025238/ses-2/sub-0025238_ses-2_run-1_T1w</fnames>
- </filedata>
- <parameter>
- <opts>
- <tpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii</item>
- </tpm>
- <ngaus>[1 1 2 3 4 2]</ngaus>
- <affreg>mni</affreg>
- <warpreg>[0 0.001 0.5 0.05 0.2]</warpreg>
- <tol>0.0001</tol>
- <accstr>0.5</accstr>
- <biasstr>0.5</biasstr>
- <biasreg>0.001</biasreg>
- <biasfwhm>60</biasfwhm>
- <samp>3</samp>
- <redspmres>0</redspmres>
- <fwhm>1</fwhm>
- <biasacc>0</biasacc>
- </opts>
- <extopts>
- <uhrlim>1.4</uhrlim>
- <gcutstr>2</gcutstr>
- <cleanupstr>0.5</cleanupstr>
- <spm_kamap>0</spm_kamap>
- <NCstr>-Inf</NCstr>
- <LASstr>0.5</LASstr>
- <BVCstr>0.5</BVCstr>
- <regstr>0.5</regstr>
- <WMHC>2</WMHC>
- <WMHCstr>0.5</WMHCstr>
- <SLC>0</SLC>
- <mrf>1</mrf>
- <restype>optimal</restype>
- <resval>[1 0.3]</resval>
- <bids_folder>../derivatives/CAT12.8.1_2040</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>1</nproc>
- <species>human</species>
- <APP>1070</APP>
- <setCOM>1</setCOM>
- <vox>1.5</vox>
- <bb>12</bb>
- <shootingsurf>Template_T1</shootingsurf>
- <pth_templates>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
- <darteltpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- </darteltpm>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <shootingT1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
- </shootingT1>
- <brainmask>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
- </brainmask>
- <T1>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
- </T1>
- <cat12atlas>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat.nii</item>
- </cat12atlas>
- <pbtres>0.5</pbtres>
- <SRP>22</SRP>
- <reduce_mesh>1</reduce_mesh>
- <vdist>2</vdist>
- <pbtlas>0</pbtlas>
- <thick_measure>1</thick_measure>
- <thick_limit>5</thick_limit>
- <close_parahipp>0</close_parahipp>
- <scale_cortex>0.7</scale_cortex>
- <add_parahipp>0.1</add_parahipp>
- <colormap>BCGWHw</colormap>
- <report/>
- <verb>2</verb>
- <ignoreErrors>1</ignoreErrors>
- <expertgui>1</expertgui>
- <subfolders>1</subfolders>
- <experimental>0</experimental>
- <print>2</print>
- <fontsize>10</fontsize>
- <send_info>1</send_info>
- <gifti_dat>1</gifti_dat>
- <atlas>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
- <td>0</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
- <td>0</td>
- <td>
- <item>csf</item>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- </td>
- <td>[false]</td>
- </tr>
- <tr>
- <td>/var/lib/condor/execute/dir_3468898/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>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.654642470678517</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0734745711088181</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0742356553673744</SurfacePositionRMSE>
- <res_vx_vol>[1 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1</res_RMS>
- <res_BB>178.377655029297</res_BB>
- <tissue_mn>[14.9119997024536 105.802001953125 308.877014160156 477.738006591797]</tissue_mn>
- <tissue_mnr>[0.0312137603759766 0.221464484930038 0.646540582180023 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[10.7416847251109 55.567996647609 52.6572465987917 31.891422874801]</tissue_std>
- <tissue_stdr>[0.0232089050114155 0.12006238847971 0.113773308694363 0.0689058527350426]</tissue_stdr>
- <contrast>172.159484863281</contrast>
- <contrastr>0.360363811254501</contrastr>
- <res_ECR>0.373448133468628</res_ECR>
- <NCR>0.140123546123505</NCR>
- <ICR>0.265816181898117</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2 2 2]</res_vx_vol>
- <res_RMS>2</res_RMS>
- <res_ECR>2.80330681800842</res_ECR>
- <res_BB>10.5</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>2.67787599563599</contrastr>
- <NCR>2.34257173538208</NCR>
- <ICR>1.11908769607544</ICR>
- <SurfaceEulerNumber>1.71428571428571</SurfaceEulerNumber>
- <SurfaceDefectArea>1.16366061766963</SurfaceDefectArea>
- <SurfaceDefectNumber>1.6</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.46949148178101</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.48471307754517</SurfacePositionRMSE>
- <SIQR>2.52625881390117</SIQR>
- <IQR>2.21596280583478</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
- <res_BB>brain next to the image boundary</res_BB>
- <tissue_mn>mean within the tissue classes</tissue_mn>
- <tissue_std>standard deviation within the tissue classes</tissue_std>
- <contrast>contrast between tissue classes</contrast>
- <contrastr>contrast between tissue classes</contrastr>
- <NCR>noise to contrast ratio</NCR>
- <ICR>inhomogeneity to contrast ratio</ICR>
- <SurfaceEulerNumber>average Euler number (characteristic)</SurfaceEulerNumber>
- <SurfaceDefectArea>average area of topological defects</SurfaceDefectArea>
- <SurfaceDefectNumber>average number of defects</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>RMSE of the expected boundary intensity Ym of the IS, OS, and CS</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>RMSE of the expected boundary position Ypp of the IS, OS, and CS</SurfacePositionRMSE>
- <SurfaceSelfIntersections>Percentual area of self-intersections of the IS and OS.</SurfaceSelfIntersections>
- </qualitymeasures>
- <subjectmeasures>
- <vol_TIV>total intracranial volume (GM+WM+VT)</vol_TIV>
- <vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
- <vol_rel_WMH>relative WMH volume</vol_rel_WMH>
- <surf_TSA>total surface area</surf_TSA>
- </subjectmeasures>
- </ratings_help>
- <software>
- <version_segment>1639</version_segment>
- <system>LINUX</system>
- <version_spm>7771</version_spm>
- <version_matlab>9.3</version_matlab>
- <version_cat>12.8.1</version_cat>
- <revision_cat>2040</revision_cat>
- <function>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_vol_qa.m</function>
- <markdefs>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
- <qamethod>cat12</qamethod>
- <date>20231031-020735</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>16</SurfaceEulerNumber>
- <SurfaceDefectArea>0.654642470678517</SurfaceDefectArea>
- <SurfaceDefectNumber>12</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0734745711088181</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0742356553673744</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>16</EC_abs>
- <defect_size>0.654642470678517</defect_size>
- <vol_abs_CGW>[183.627231372549 800.281011764706 500.126541176471 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.785392156862745</vol_abs_WMH>
- <vol_rel_WMH>0.000529227593021642</vol_rel_WMH>
- <surf_TSA>2073.79023379512</surf_TSA>
- <vol_TIV>1484.03478431373</vol_TIV>
- <vol_rel_CGW>[0.123735126233894 0.539260278952819 0.337004594813287 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.75861025663577 0.659013334961871]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.78137445449829 0.854917354946884 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.10967430364454 0.2842667716178 0.283663360607358;2.78947974316003 0.189741294691448 0.422575717245131;3.47720069025932 0.288861200007341 0.293760922147511]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.898824407370172 0.366350788738048 0.637496486461164;4.40717245904504 0.28117399522621 0.362503513538836]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.16640556210147</vol_TIV>
- <vol_rel_CGW>[0.5 7.53484696395149 3.90238137236507 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05292275930216</vol_rel_WMH>
- <surf_TSA>8.62318623382458</surf_TSA>
- <SQR>6.16571548154279</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 9371.648 0.355799498616816]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00188510562293231 0.000984748010523617 0.307662904262543]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[910.709992156863 456.884023529412 298.786082352941 469.379968627451 1090.54029411765 6689.12934117647]</SPMvols0>
- <SPMvols1>[818.777117647059 430.503152941176 167.118968627451 359.053011764706 797.249745098039 6798.98509019608]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[108.783996582031 321.825286865234 465.481201171875]</T3th>
- <Tth>
- <T3th>[-6.91064977645874 -6.91064500808716 9.73148822784424 108.783996582031 321.825286865234 465.481201171875 643.829833984375 1037.48266601562]</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>[0.0185897406190634 0.0676454976201057 0.0741084367036819 0 0]</dtc>
- <ll>[0.0818852443321078 0 0.0818852443321078 0;0.193792281316824 0.00959630373145352 0.203388585048277 2046.392578125;0.193792281316824 0.00959630373145352 0.203388585048277 2046.392578125]</ll>
- <rmsdtc>[0.0429034307599068 0.0894943848252296 0.0990547686815262]</rmsdtc>
- <rmsgdt>[0.0310371685773134 0.0409213006496429 0.0505424477159977]</rmsgdt>
- <rmsdt>0.0990547686815262</rmsdt>
- <dt>0.0741084367036819</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>[0.00872341450303793 0.0321648456156254 0.0456366799771786 0.0545281879603863 0.0616789199411869 0.0691069811582565]</dtc>
- <ll>[0.0817771708100379 0 0.0817771708100379 0;0.213987240537241 0.0131523885836386 0.227139629120879 6732.37890625;0.194355823926793 0.016123284166097 0.21047910809289 11604.12109375;0.174099363379555 0.0186315194154397 0.192730882794995 20089.845703125;0.157172805460076 0.0216931854591383 0.178865990919214 37949.0390625;0.157172805460076 0.0216931854591383 0.178865990919214 37949.0390625]</ll>
- <rmsdtc>[0.0105661461129785 0.0382757037878036 0.057610347867012 0.0832716375589371 0.10773703455925 0.114758960902691]</rmsdtc>
- <rmsgdt>[0.00305191962979734 0.0119153102859855 0.0275007542222738 0.0488513000309467 0.0677630454301834 0.0735822916030884]</rmsgdt>
- <rmsdt>0.114758960902691</rmsdt>
- <dt>0.0691069811582565</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025238/ses-2/sub-0025238_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 67s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 7s</item>
- <item>Initial correction 7s</item>
- <item>Refine background 3s</item>
- <item>Final correction 6s</item>
- <item>Final scaling 6s</item>
- <item>41s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 88s</item>
- <item>SPM preprocessing 1 (estimate 2): 89s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 18s</item>
- <item>Update Segmentation 21s</item>
- <item>Update Skull-Stripping 42s</item>
- <item>Update probability maps 8s</item>
- <item>90s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 39s</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) 18s</item>
- <item>Estimate local tissue thresholds (WM) 22s</item>
- <item>Estimate local tissue thresholds (GM) 36s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 46s</item>
- <item>131s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 8s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 17s</item>
- <item>Blood vessel detection 13s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 35s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 2s</item>
- <item>Side alignment 4s</item>
- <item>Final corrections 4s</item>
- <item>87s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.05): 39s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.07,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 4s</item>
- <item>15s</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 | 0.0818 0.0000 0.0818 | 32.0000</item>
- <item>2 | 2.50 | 0.0791 0.0012 0.0803 | 29.4886</item>
- <item>3 | 2.50 | 0.0783 0.0018 0.0801 | 26.9772</item>
- <item>4 | 2.50 | 0.0779 0.0020 0.0799 | 24.6107</item>
- <item>5 | 2.50 | 0.0776 0.0022 0.0798 | 22.6548</item>
- <item>6 | 2.50 | 0.0773 0.0023 0.0796 | 20.6989</item>
- <item>7 | 2.50 | 0.0771 0.0024 0.0794 | 18.9688</item>
- <item>8 | 2.50 | 0.0768 0.0025 0.0792 | 17.4455</item>
- <item>9 | 2.50 | 0.0765 0.0025 0.0790 | 15.9223</item>
- <item>10 | 2.50 | 0.0762 0.0026 0.0788 | 14.6627</item>
- <item>11 | 2.50 | 0.0759 0.0027 0.0786 | 13.4764</item>
- <item>12 | 2.50 | 0.0756 0.0028 0.0783 | 12.3015</item>
- <item>13 | 2.50 | 0.0752 0.0029 0.0781 | 11.3776</item>
- <item>14 | 2.50 | 0.0749 0.0029 0.0779 | 10.4537</item>
- <item>15 | 2.25 | 0.0742 0.0030 0.0771 | 9.5920</item>
- <item>16 | 2.25 | 0.0713 0.0044 0.0757 | 8.8725</item>
- <item>29 | 2.00 | 0.0728 0.0020 0.0748 | 3.3283</item>
- <item>30 | 2.00 | 0.0668 0.0044 0.0712 | 3.1221</item>
- <item>31 | 2.00 | 0.0648 0.0054 0.0702 | 2.9160</item>
- <item>43 | 1.75 | 0.0639 0.0031 0.0670 | 1.5785</item>
- <item>44 | 1.75 | 0.0595 0.0054 0.0649 | 1.5194</item>
- <item>45 | 1.75 | 0.0580 0.0062 0.0642 | 1.4626</item>
- <item>57 | 1.50 | 0.0566 0.0045 0.0611 | 1.0900</item>
- <item>58 | 1.50 | 0.0534 0.0066 0.0600 | 1.0730</item>
- <item>59 | 1.50 | 0.0524 0.0072 0.0596 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 204s</item>
- <item>Prepare output 13s</item>
- <item>217s</item>
- <item>Jacobian determinant (RMS): 0.011 0.038 0.058 0.083 0.108 | 0.114759</item>
- <item>Template Matching: 0.082 0.214 0.194 0.174 0.157 | 0.157173</item>
- <item>Write result maps: 40s</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: 22s</item>
- <item>PBT2x thickness: 65s</item>
- <item>131s</item>
- <item>Create initial surface 112s</item>
- <item>Topology correction: 122s</item>
- <item>Surface refinement: 124s</item>
- <item>Reduction of surface collisions with optimization: 96s</item>
- <item>Spherical mapping with areal smoothing 115s</item>
- <item>Spherical registration 362s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 39s</item>
- <item>CSF distance: 21s</item>
- <item>PBT2x thickness: 65s</item>
- <item>132s</item>
- <item>Create initial surface 111s</item>
- <item>Topology correction: 121s</item>
- <item>Surface refinement: 83s</item>
- <item>Reduction of surface collisions with optimization: 94s</item>
- <item>Spherical mapping with areal smoothing 113s</item>
- <item>Spherical registration 367s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.7591 0.6570 mm</item>
- <item>Surface intensity / position RMSE: 0.0735 / 0.0742</item>
- <item>Euler number / defect number / defect size: 16.0 / 12.0 / 0.65%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/surf/lh.thickness.sub-0025238_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/surf/rh.thickness.sub-0025238_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/sub-0025238_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 12s</item>
- <item>Surface and thickness estimation takes: 2208s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 9s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 32s</item>
- <item>ROI estimation of 'lpba40' atlas 10s</item>
- <item>ROI estimation of 'hammers' atlas 23s</item>
- <item>ROI estimation of 'thalamus' atlas 2s</item>
- <item>ROI estimation of 'ibsr' atlas 9s</item>
- <item>ROI estimation of 'aal3' atlas 15s</item>
- <item>ROI estimation of 'mori' atlas 22s</item>
- <item>ROI estimation of 'anatomy3' atlas 28s</item>
- <item>ROI estimation of 'julichbrain' atlas 36s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 14s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 56s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 81s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 8s</item>
- <item>369s</item>
- <item>Quality check: 13s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/report/catreport_sub-0025238_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 61 minute(s) and 28 second(s).</item>
- <item>Image Quality Rating (IQR): 82.84% (B-)</item>
- <item>GM volume (GMV): 53.93% (800.28 / 1484.03 ml)</item>
- <item>GM thickness (GMT): 2.76 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3468898/ds/UPSM_1/sub-0025238/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|