123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.10411287931303 -0.0287204106025774 0.107133237553525 11.386886245073;0.00632227512195173 1.04207242940056 0.255204111693064 -5.30648551889619;-0.119836028618449 -0.291144423851475 1.15694377628597 25.1015189618722;0 0 0 1]</Affine>
- <Affine0>[1.10411287931303 -0.0287204106025774 0.107133237553525 11.386886245073;0.00632227512195173 1.04207242940056 0.255204111693064 -5.30648551889619;-0.119836028618449 -0.291144423851475 1.15694377628597 25.1015189618722;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[228.652292999971 361.362070473795 39.0047527146709 111.298309018161 89.5168965408998 27.2127630885744 46.9071873872709 211.164997016055 809.815620080157 432.158259217435 194.333766727531 89.0911683131807 27.9880507643729]</mn>
- <vr>[2080.69972717231;538.610012579502;182.046108613653;1507.81334507486;854.82828451993;89.9165428429635;240.064467244117;4213.31113553844;15323.4005991707;4534.51974291405;3246.84427294768;1323.70191147609;136.433240365607]</vr>
- <ll>-5.58659648895264</ll>
- <Affine_translation>[11.386886245073 -5.30648551889619 25.1015189618722]</Affine_translation>
- <Affine_rotation>[0.275174118457152 0.102535949827624 -0.0348036043725012]</Affine_rotation>
- <Affine_scaling>[1.11061509767456 1.08232506333459 1.18751345480389]</Affine_scaling>
- <Affine_shearing>[0.0079185690476893 -0.0151953041964247 -0.0630214430897562]</Affine_shearing>
- <Affine0_translation>[11.386886245073 -5.30648551889619 25.1015189618722]</Affine0_translation>
- <Affine0_rotation>[0.275174118457152 0.102535949827624 -0.0348036043725012]</Affine0_rotation>
- <Affine0_scaling>[1.11061509767456 1.08232506333459 1.18751345480389]</Affine0_scaling>
- <Affine0_shearing>[0.0079185690476893 -0.0151953041964247 -0.0630214430897562]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1</path>
- <file>sub-0025038_ses-1_run-2_T1w</file>
- <fname>/var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/sub-0025038_ses-1_run-2_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/sub-0025038_ses-1_run-2_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/mri/msub-0025038_ses-1_run-2_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/mri/p0sub-0025038_ses-1_run-2_T1w.nii</Fp0>
- <fnames>..s/NYU_2/sub-0025038/ses-1/sub-0025038_ses-1_run-2_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_1362078/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>92</SurfaceEulerNumber>
- <SurfaceDefectArea>2.6590073976108</SurfaceDefectArea>
- <SurfaceDefectNumber>42</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0802339091897011</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0951855033636093</SurfacePositionRMSE>
- <res_vx_vol>[1.33000183105469 1 1]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>1.12084861758235</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[9.54199981689453 30.5209999084473 194.755996704102 361.700012207031]</tissue_mn>
- <tissue_mnr>[0.0263809766620398 0.0843820795416832 0.538446187973022 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[7.17055474602218 46.6070710427477 46.0304102902797 34.6981425367069]</tissue_std>
- <tissue_stdr>[0.0203617531806231 0.132347032427788 0.130709528923035 0.098530039191246]</tissue_stdr>
- <contrast>122.443183898926</contrast>
- <contrastr>0.338521361351013</contrastr>
- <res_ECR>0.444187939167023</res_ECR>
- <NCR>0.167063057422638</NCR>
- <ICR>0.438786208629608</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.66000366210938 2 2]</res_vx_vol>
- <res_RMS>2.24169723516471</res_RMS>
- <res_ECR>3.16422414779663</res_ECR>
- <res_BB>NaN</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>0.5</contrast>
- <contrastr>3.00551295280457</contrastr>
- <NCR>2.72930026054382</NCR>
- <ICR>1.5480809211731</ICR>
- <SurfaceEulerNumber>5.59183673469388</SurfaceEulerNumber>
- <SurfaceDefectArea>1.6647518494027</SurfaceDefectArea>
- <SurfaceDefectNumber>3.1</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.6046781539917</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.90371012687683</SurfacePositionRMSE>
- <SIQR>2.86887103523274</SIQR>
- <IQR>2.56236509687258</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>20231031-031048</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>92</SurfaceEulerNumber>
- <SurfaceDefectArea>2.6590073976108</SurfaceDefectArea>
- <SurfaceDefectNumber>42</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0802339091897011</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0951855033636093</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>92</EC_abs>
- <defect_size>2.6590073976108</defect_size>
- <vol_abs_CGW>[181.175678431373 661.450631372549 432.099011764706 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.530909803921569</vol_abs_WMH>
- <vol_rel_WMH>0.000416489572254085</vol_rel_WMH>
- <surf_TSA>1775.90149477115</surf_TSA>
- <vol_TIV>1274.72532156863</vol_TIV>
- <vol_rel_CGW>[0.142129190787883 0.518896596922224 0.338974212289893 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.55410802201372 0.697320577198511]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.59050059318542 0.837190243879131 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[1.82918920148039 0.294247945256958 0.280364749183243;2.59077894315781 0.207528256499919 0.420509215224074;3.3116437498966 0.299436500936706 0.299126035592683]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.775787941630029 0.266220066606072 0.626615118526808;4.25023480338687 0.2890868669446 0.373384881473192]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>1.3648828769126</vol_TIV>
- <vol_rel_CGW>[0.5 7.16911991598823 3.93775524945928 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.04164895722541</vol_rel_WMH>
- <surf_TSA>8.57219826390405</surf_TSA>
- <SQR>5.86870767233609</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11156.864 0.458668904074583]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00203517032787204 0.00169337599072605 0.0977553799748421]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[782.168003921569 388.586878431373 282.593674509804 602.819219607843 1112.24130980392 8473.82857647059]</SPMvols0>
- <SPMvols1>[700.360376470588 362.739133333333 157.583756862745 425.215756862745 860.95917254902 8634.49863921569]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[45.959098815918 216.002502441406 363.121307373047]</T3th>
- <Tth>
- <T3th>[-69.4718704223633 -69.4718627929688 -11.7563819885254 45.959098815918 216.002502441406 363.121307373047 521.702392578125 1199.25256347656]</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>[0.0196397006511688 0.0703161582350731 0.0773243010044098 0 0]</dtc>
- <ll>[0.0801151454234037 0 0.0801151454234037 0;0.187804772788021 0.00937243755839738 0.197177210346419 1998.65356445312;0.187804772788021 0.00937243755839738 0.197177210346419 1998.65356445312]</ll>
- <rmsdtc>[0.0437232591211796 0.0932556912302971 0.103800371289253]</rmsdtc>
- <rmsgdt>[0.0313867777585983 0.0423699095845222 0.0524007230997086]</rmsgdt>
- <rmsdt>0.103800371289253</rmsdt>
- <dt>0.0773243010044098</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>[0.00886813178658485 0.0330362394452095 0.0467968657612801 0.0543754622340202 0.05954460054636 0.0665775910019875]</dtc>
- <ll>[0.0812433951013045 0 0.0812433951013045 0;0.211132173382173 0.0129616052350427 0.224093778617216 6634.7216796875;0.191182592828798 0.0155904429914327 0.206773035820231 11220.62890625;0.172594409156502 0.017339387623786 0.189933796780288 18696.576171875;0.159712905285554 0.0181607455370643 0.177873650822618 31769.5546875;0.159712905285554 0.0181607455370643 0.177873650822618 31769.5546875]</ll>
- <rmsdtc>[0.01066127512604 0.0394228585064411 0.059156134724617 0.0826943293213844 0.104566089808941 0.109661482274532]</rmsdtc>
- <rmsgdt>[0.0031917707528919 0.0124777425080538 0.0270233899354935 0.0469570644199848 0.0646767169237137 0.0691941827535629]</rmsgdt>
- <rmsdt>0.109661482274532</rmsdt>
- <dt>0.0665775910019875</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0025038/ses-1/sub-0025038_ses-1_run-2_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 5s</item>
- <item>Refine background 3s</item>
- <item>Final correction 4s</item>
- <item>Final scaling 4s</item>
- <item>34s</item>
- <item>Correct center-of-mass 4s</item>
- <item>Affine registration 9s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 13s</item>
- <item>Use initial fine affine registration. 61s</item>
- <item>SPM preprocessing 1 (estimate 2): 54s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 15s</item>
- <item>Update Segmentation 17s</item>
- <item>Update Skull-Stripping 37s</item>
- <item>Update probability maps 8s</item>
- <item>76s</item>
- <item>Global intensity correction: 15s</item>
- <item>SANLM denoising after intensity normalization (medium): 23s</item>
- <item>Fast Optimized Shooting registration 29s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 3s</item>
- <item>Prepare partitions 2s</item>
- <item>Prepare segments (LASmod = 1.10) 12s</item>
- <item>Estimate local tissue thresholds (WM) 16s</item>
- <item>Estimate local tissue thresholds (GM) 24s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 38s</item>
- <item>99s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 7s</item>
- <item>Major structures 3s</item>
- <item>Ventricle detection 10s</item>
- <item>Blood vessel detection 8s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.00) 21s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 1s</item>
- <item>Side alignment 3s</item>
- <item>Final corrections 4s</item>
- <item>58s</item>
- <item>Blood vessel correction (BVCstr=0.50): 2s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 28s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.99 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 3s</item>
- <item>Level 1 cleanup (brain masking) 2s</item>
- <item>Level 2 cleanup (CSF correction) 1s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 2s</item>
- <item>9s</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 | 0.0812 0.0000 0.0812 | 32.0000</item>
- <item>2 | 2.50 | 0.0788 0.0011 0.0799 | 29.4886</item>
- <item>3 | 2.50 | 0.0780 0.0017 0.0797 | 26.9772</item>
- <item>4 | 2.50 | 0.0777 0.0019 0.0796 | 24.6107</item>
- <item>5 | 2.50 | 0.0774 0.0021 0.0794 | 22.6548</item>
- <item>6 | 2.50 | 0.0771 0.0022 0.0793 | 20.6989</item>
- <item>7 | 2.50 | 0.0769 0.0023 0.0791 | 18.9688</item>
- <item>8 | 2.50 | 0.0766 0.0024 0.0789 | 17.4455</item>
- <item>9 | 2.50 | 0.0763 0.0024 0.0787 | 15.9223</item>
- <item>10 | 2.50 | 0.0760 0.0025 0.0785 | 14.6627</item>
- <item>11 | 2.50 | 0.0757 0.0026 0.0783 | 13.4764</item>
- <item>12 | 2.50 | 0.0754 0.0027 0.0781 | 12.3015</item>
- <item>13 | 2.50 | 0.0751 0.0028 0.0779 | 11.3776</item>
- <item>14 | 2.50 | 0.0748 0.0028 0.0776 | 10.4537</item>
- <item>15 | 2.25 | 0.0732 0.0029 0.0761 | 9.5920</item>
- <item>16 | 2.25 | 0.0704 0.0043 0.0747 | 8.8725</item>
- <item>29 | 2.00 | 0.0714 0.0019 0.0733 | 3.3283</item>
- <item>30 | 2.00 | 0.0656 0.0043 0.0699 | 3.1221</item>
- <item>31 | 2.00 | 0.0637 0.0052 0.0689 | 2.9160</item>
- <item>43 | 1.75 | 0.0628 0.0030 0.0657 | 1.5785</item>
- <item>44 | 1.75 | 0.0588 0.0051 0.0639 | 1.5194</item>
- <item>45 | 1.75 | 0.0575 0.0058 0.0633 | 1.4626</item>
- <item>57 | 1.50 | 0.0561 0.0042 0.0603 | 1.0900</item>
- <item>58 | 1.50 | 0.0532 0.0061 0.0593 | 1.0730</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 124s</item>
- <item>Prepare output 8s</item>
- <item>133s</item>
- <item>Jacobian determinant (RMS): 0.011 0.039 0.059 0.083 0.105 | 0.109661</item>
- <item>Template Matching: 0.081 0.211 0.191 0.173 0.160 | 0.159713</item>
- <item>Write result maps: 48s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 20s</item>
- <item>CSF distance: 11s</item>
- <item>PBT2x thickness: 34s</item>
- <item>69s</item>
- <item>Create initial surface 65s</item>
- <item>Topology correction: 71s</item>
- <item>Surface refinement: 62s</item>
- <item>Reduction of surface collisions with optimization: 53s</item>
- <item>Spherical mapping with areal smoothing 62s</item>
- <item>Spherical registration 247s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 22s</item>
- <item>CSF distance: 12s</item>
- <item>PBT2x thickness: 35s</item>
- <item>74s</item>
- <item>Create initial surface 68s</item>
- <item>Topology correction: 74s</item>
- <item>Surface refinement: 61s</item>
- <item>Reduction of surface collisions with optimization: 51s</item>
- <item>Spherical mapping with areal smoothing 61s</item>
- <item>Spherical registration 248s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.5544 0.6960 mm</item>
- <item>Surface intensity / position RMSE: 0.0802 / 0.0952</item>
- <item>Euler number / defect number / defect size: 92.0 / 42.0 / 2.66%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/surf/lh.thickness.sub-0025038_ses-1_run-2_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/surf/rh.thickness.sub-0025038_ses-1_run-2_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/sub-0025038_ses-1_run-2_T1w.nii</item>
- <item>Surface ROI estimation: 7s</item>
- <item>Surface and thickness estimation takes: 1344s</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 28s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 11s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 20s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 46s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 68s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 6s</item>
- <item>Write results 7s</item>
- <item>291s</item>
- <item>Quality check: 9s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/report/catreport_sub-0025038_ses-1_run-2_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 40 minute(s) and 34 second(s).</item>
- <item>Image Quality Rating (IQR): 79.38% (C+)</item>
- <item>GM volume (GMV): 51.89% (661.45 / 1274.73 ml)</item>
- <item>GM thickness (GMT): 2.55 0.70 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_1362078/ds/NYU_2/sub-0025038/ses-1/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|