123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[0.998853232710454 0.00393510043122396 -0.0280068685781534 -0.366561023401768;-0.0136033445972585 1.03194225958893 0.159926924071713 -29.9106064804314;0.0321948254749458 -0.172320958644591 1.0629838510963 -3.59873208356498;0 0 0 1]</Affine>
- <Affine0>[0.998853232710454 0.00393510043122396 -0.0280068685781534 -0.366561023401768;-0.0136033445972585 1.03194225958893 0.159926924071713 -29.9106064804314;0.0321948254749458 -0.172320958644591 1.0629838510963 -3.59873208356498;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[236.749941550305 347.47559933003 56.3454414841921 146.749309527644 95.0265122182081 29.4704640954739 55.9158964220884 219.862254227541 434.301109938938 377.391747288976 256.300588313995 87.1432429965217 27.4467000504124]</mn>
- <vr>[2017.53209441161;313.385102302599;451.556653825866;2029.59207926471;852.49176914994;150.277019529416;269.260287116413;8299.15329256208;10526.6780971771;13043.6013444107;2637.37777492934;1449.79068181932;165.074591777829]</vr>
- <ll>-5.59267473220825</ll>
- <Affine_translation>[-0.366561023401768 -29.9106064804314 -3.59873208356498]</Affine_translation>
- <Affine_rotation>[0.165571482766759 -0.0295377798167128 0.0187346601313918]</Affine_rotation>
- <Affine_scaling>[0.999464525767533 1.04612115905179 1.07516365258299]</Affine_scaling>
- <Affine_shearing>[-0.0156719008686635 0.0040766520081197 -0.0166172709938218]</Affine_shearing>
- <Affine0_translation>[-0.366561023401768 -29.9106064804314 -3.59873208356498]</Affine0_translation>
- <Affine0_rotation>[0.165571482766759 -0.0295377798167128 0.0187346601313918]</Affine0_rotation>
- <Affine0_scaling>[0.999464525767533 1.04612115905179 1.07516365258299]</Affine0_scaling>
- <Affine0_shearing>[-0.0156719008686635 0.0040766520081197 -0.0166172709938218]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2</path>
- <file>sub-0025490_ses-2_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/sub-0025490_ses-2_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/sub-0025490_ses-2_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/mri/msub-0025490_ses-2_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/mri/p0sub-0025490_ses-2_run-1_T1w.nii</Fp0>
- <fnames>..IPCAS_1/sub-0025490/ses-2/sub-0025490_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_2807912/ds/code/Tian_Subcortex_S2_7T.nii</td>
- <td>1</td>
- <td>
- <item>gm</item>
- <item>wm</item>
- <item>csf</item>
- </td>
- <td>[false]</td>
- </tr>
- </atlas>
- <satlas>
- <tr>
- <td>Desikan</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_a2009s.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>Destrieux</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_DK40.freesurfer.annot</td>
- <td>0</td>
- <td>1</td>
- </tr>
- <tr>
- <td>HCP</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.aparc_HCP_MMP1.freesurfer.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_100P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_100Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_200P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_200Parcels_17Networks_order.annot</td>
- <td>0</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_400P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_400Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- <tr>
- <td>Schaefer2018_600P_17N</td>
- <td>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/atlases_surfaces/lh.Schaefer2018_600Parcels_17Networks_order.annot</td>
- <td>1</td>
- <td>0</td>
- </tr>
- </satlas>
- <LAB>
- <NB>0</NB>
- <CT>1</CT>
- <CB>3</CB>
- <BG>5</BG>
- <BV>7</BV>
- <TH>9</TH>
- <ON>11</ON>
- <MB>13</MB>
- <BS>13</BS>
- <VT>15</VT>
- <NV>17</NV>
- <HC>19</HC>
- <HD>21</HD>
- <HI>23</HI>
- <PH>25</PH>
- <LE>27</LE>
- </LAB>
- <new_release>0</new_release>
- <lazy>0</lazy>
- <affmod>0</affmod>
- <regmethod>
- <shooting>
- <shootingtpm>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- </shootingtpm>
- <regstr>0.5</regstr>
- </shooting>
- </regmethod>
- <restypes>
- <optimal>[1 0.3]</optimal>
- </restypes>
- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
- <darteltpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
- </darteltpms>
- <shootingtpms>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </shootingtpms>
- <templates>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
- </templates>
- <inv_weighting>0</inv_weighting>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.801016542488464</SurfaceDefectArea>
- <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0681978911161423</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0704369321465492</SurfacePositionRMSE>
- <res_vx_vol>[1.33000004291534 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1.12084791031237</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[4.22200012207031 36.4529991149902 199.113998413086 344.054992675781]</tissue_mn>
- <tissue_mnr>[0.0122712943702936 0.105951085686684 0.578727245330811 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[3.22344845098778 38.3120314102327 39.8614120599644 27.4462466453122]</tissue_std>
- <tissue_stdr>[0.00948538910597563 0.112737819552422 0.117297060787678 0.0807639211416245]</tissue_stdr>
- <contrast>119.742156982422</contrast>
- <contrastr>0.348032027482986</contrastr>
- <res_ECR>0.470777928829193</res_ECR>
- <NCR>0.189941078424454</NCR>
- <ICR>0.312136471271515</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000008583069 2 2]</res_vx_vol>
- <res_RMS>2.24169582062474</res_RMS>
- <res_ECR>3.29988741874695</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[8.62399959564209 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>2.86285281181335</contrastr>
- <NCR>3.05772423744202</NCR>
- <ICR>1.23396944999695</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>1.20025413562212</SurfaceDefectArea>
- <SurfaceDefectNumber>1.925</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.36395788192749</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.40873861312866</SurfacePositionRMSE>
- <SIQR>3.04785446755071</SIQR>
- <IQR>2.83217888884104</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>20231031-000412</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>0.801016542488464</SurfaceDefectArea>
- <SurfaceDefectNumber>18.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0681978911161423</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0704369321465492</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>0.801016542488464</defect_size>
- <vol_abs_CGW>[314.407231372549 762.063043137255 626.775964705882 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.700925490196078</vol_abs_WMH>
- <vol_rel_WMH>0.000411523286567679</vol_rel_WMH>
- <surf_TSA>2110.10078550085</surf_TSA>
- <vol_TIV>1703.24623921569</vol_TIV>
- <vol_rel_CGW>[0.184592940312217 0.447418010145245 0.367989049542538 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.51558248282264 0.656327226314304]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.48301672935486 0.809270592268053 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.88088247775655 0.263291792127508 0.32061771623294;2.54196757491843 0.193791483538425 0.436770890151848;3.28102410246531 0.298704168691428 0.242611393615212]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.879292835893196 0.296104175589813 0.482099795956223;4.31132155251196 0.33865536726593 0.517900204043777]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.90421317490767</vol_TIV>
- <vol_rel_CGW>[1.1651030946878 5.88538092933271 4.45885505643926 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04115232865677</vol_rel_WMH>
- <surf_TSA>8.62354963163229</surf_TSA>
- <SQR>4.8752553649221</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.849 0.368139390960733]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00192842003889382 0.00174047681502998 0.0192827600985765]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[938.149749019608 542.938364705882 665.367976470588 361.342435294118 994.967874509804 8290.53462352941]</SPMvols0>
- <SPMvols1>[777.784215686274 509.118243137255 374.81462745098 334.685666666667 829.316690196078 8315.44070980392]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[64.6681976318359 219.769805908203 347.963714599609]</T3th>
- <Tth>
- <T3th>[-79.3907318115234 -69.8132934570312 -2.57254791259766 64.6681976318359 219.769805908203 347.963714599609 489.611480712891 918.476135253906]</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>[0.0189323741942644 0.0702273100614548 0.0773243978619576 0 0]</dtc>
- <ll>[0.0853107295164159 0 0.0853107295164159 0;0.203145552654656 0.00992623840918203 0.213071791063838 2116.75048828125;0.203145552654656 0.00992623840918203 0.213071791063838 2116.75048828125]</ll>
- <rmsdtc>[0.0440806150436401 0.0934937074780464 0.104251272976398]</rmsdtc>
- <rmsgdt>[0.0321040637791157 0.0458094701170921 0.0565610304474831]</rmsgdt>
- <rmsdt>0.104251272976398</rmsdt>
- <dt>0.0773243978619576</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>[0.00743263121694326 0.0270698629319668 0.0380230620503426 0.0453385673463345 0.0514137893915176 0.0568121522665024]</dtc>
- <ll>[0.0843888507612103 0 0.0843888507612103 0;0.222120375457875 0.0122161153083028 0.234336490766178 6253.1240234375;0.201822851536448 0.0152568337990578 0.217079685335506 10980.5263671875;0.182516346177031 0.0174596900613899 0.199976036238421 18826.294921875;0.166063467464828 0.0203928520287215 0.18645631949355 35674.296875;0.166063467464828 0.0203928520287215 0.18645631949355 35674.296875]</ll>
- <rmsdtc>[0.00889508333057165 0.0324374362826347 0.0483850948512554 0.0688541457056999 0.0903940498828888 0.0971941724419594]</rmsdtc>
- <rmsgdt>[0.00298768817447126 0.0114694377407432 0.0253003761172295 0.0435973517596722 0.0611529015004635 0.0668125748634338]</rmsgdt>
- <rmsdt>0.0971941724419594</rmsdt>
- <dt>0.0568121522665024</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025490/ses-2/sub-0025490_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 34s</item>
- <item>Internal resampling (1.33x1.00x1.00mm > 1.00x1.00x1.00mm): 1s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 6s</item>
- <item>Estimate background 6s</item>
- <item>Initial correction 6s</item>
- <item>Refine background 3s</item>
- <item>Final correction 5s</item>
- <item>Final scaling 5s</item>
- <item>37s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 89s</item>
- <item>SPM preprocessing 1 (estimate 2): 76s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 17s</item>
- <item>Update Segmentation 20s</item>
- <item>Update Skull-Stripping 42s</item>
- <item>Update probability maps 8s</item>
- <item>87s</item>
- <item>Global intensity correction: 16s</item>
- <item>SANLM denoising after intensity normalization (medium): 30s</item>
- <item>Fast Optimized Shooting registration 32s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 4s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.00) 15s</item>
- <item>Estimate local tissue thresholds (WM) 18s</item>
- <item>Estimate local tissue thresholds (GM) 27s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 39s</item>
- <item>108s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 4s</item>
- <item>Ventricle detection 15s</item>
- <item>Blood vessel detection 11s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.11) 25s</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>72s</item>
- <item>Blood vessel correction (BVCstr=0.50): 1s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 37s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.67 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 5s</item>
- <item>Level 1 cleanup (brain masking) 3s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 3s</item>
- <item>12s</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 | 0.0844 0.0000 0.0844 | 32.0000</item>
- <item>2 | 2.50 | 0.0820 0.0011 0.0831 | 29.4886</item>
- <item>3 | 2.50 | 0.0813 0.0017 0.0830 | 26.9772</item>
- <item>4 | 2.50 | 0.0809 0.0019 0.0828 | 24.6107</item>
- <item>5 | 2.50 | 0.0806 0.0020 0.0827 | 22.6548</item>
- <item>6 | 2.50 | 0.0804 0.0021 0.0825 | 20.6989</item>
- <item>7 | 2.50 | 0.0801 0.0022 0.0823 | 18.9688</item>
- <item>8 | 2.50 | 0.0799 0.0023 0.0821 | 17.4455</item>
- <item>9 | 2.50 | 0.0796 0.0023 0.0819 | 15.9223</item>
- <item>10 | 2.50 | 0.0793 0.0024 0.0817 | 14.6627</item>
- <item>11 | 2.50 | 0.0791 0.0025 0.0815 | 13.4764</item>
- <item>12 | 2.50 | 0.0788 0.0025 0.0813 | 12.3015</item>
- <item>13 | 2.50 | 0.0785 0.0026 0.0811 | 11.3776</item>
- <item>14 | 2.50 | 0.0782 0.0027 0.0809 | 10.4537</item>
- <item>15 | 2.25 | 0.0770 0.0027 0.0797 | 9.5920</item>
- <item>16 | 2.25 | 0.0740 0.0041 0.0781 | 8.8725</item>
- <item>29 | 2.00 | 0.0751 0.0018 0.0769 | 3.3283</item>
- <item>30 | 2.00 | 0.0691 0.0042 0.0733 | 3.1221</item>
- <item>31 | 2.00 | 0.0673 0.0051 0.0724 | 2.9160</item>
- <item>43 | 1.75 | 0.0663 0.0029 0.0691 | 1.5785</item>
- <item>44 | 1.75 | 0.0621 0.0051 0.0672 | 1.5194</item>
- <item>45 | 1.75 | 0.0608 0.0058 0.0667 | 1.4626</item>
- <item>57 | 1.50 | 0.0593 0.0042 0.0635 | 1.0900</item>
- <item>58 | 1.50 | 0.0563 0.0062 0.0625 | 1.0730</item>
- <item>59 | 1.50 | 0.0554 0.0068 0.0622 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 181s</item>
- <item>Prepare output 11s</item>
- <item>192s</item>
- <item>Jacobian determinant (RMS): 0.009 0.032 0.048 0.069 0.090 | 0.097194</item>
- <item>Template Matching: 0.084 0.222 0.202 0.183 0.166 | 0.166063</item>
- <item>Write result maps: 54s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 43s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 49s</item>
- <item>116s</item>
- <item>Create initial surface 91s</item>
- <item>Topology correction: 99s</item>
- <item>Surface refinement: 100s</item>
- <item>Reduction of surface collisions with optimization: 75s</item>
- <item>Spherical mapping with areal smoothing 81s</item>
- <item>Spherical registration 288s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 40s</item>
- <item>CSF distance: 17s</item>
- <item>PBT2x thickness: 48s</item>
- <item>112s</item>
- <item>Create initial surface 92s</item>
- <item>Topology correction: 99s</item>
- <item>Surface refinement: 78s</item>
- <item>Reduction of surface collisions with optimization: 78s</item>
- <item>Spherical mapping with areal smoothing 97s</item>
- <item>Spherical registration 325s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5155 0.6563 mm</item>
- <item>Surface intensity / position RMSE: 0.0682 / 0.0704</item>
- <item>Euler number / defect number / defect size: 30.0 / 18.5 / 0.80%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/surf/lh.thickness.sub-0025490_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/surf/rh.thickness.sub-0025490_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/sub-0025490_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 11s</item>
- <item>Surface and thickness estimation takes: 1840s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 13s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 47s</item>
- <item>ROI estimation of 'lpba40' atlas 14s</item>
- <item>ROI estimation of 'hammers' atlas 32s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 12s</item>
- <item>ROI estimation of 'aal3' atlas 19s</item>
- <item>ROI estimation of 'mori' atlas 27s</item>
- <item>ROI estimation of 'anatomy3' atlas 35s</item>
- <item>ROI estimation of 'julichbrain' atlas 42s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 16s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 30s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 60s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 83s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 7s</item>
- <item>Write results 8s</item>
- <item>441s</item>
- <item>Quality check: 11s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/report/catreport_sub-0025490_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 54 minute(s) and 14 second(s).</item>
- <item>Image Quality Rating (IQR): 76.68% (C+)</item>
- <item>GM volume (GMV): 44.74% (762.06 / 1703.25 ml)</item>
- <item>GM thickness (GMT): 2.52 0.66 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_2807912/ds/IPCAS_1/sub-0025490/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|