123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696 |
- <?xml version="1.0" encoding="utf-8"?>
- <S>
- <SPMpreprocessing>
- <Affine>[1.01707557711484 -0.0864850643594658 -0.0256019519120529 -0.554216003033751;0.0902972335057199 0.997454404323098 0.109665043190532 -31.0897574925538;0.0186545925836713 -0.101673624594632 1.11571940930387 2.65829758333071;0 0 0 1]</Affine>
- <Affine0>[1.01707557711484 -0.0864850643594658 -0.0256019519120529 -0.554216003033751;0.0902972335057199 0.997454404323098 0.109665043190532 -31.0897574925538;0.0186545925836713 -0.101673624594632 1.11571940930387 2.65829758333071;0 0 0 1]</Affine0>
- <lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
- <mn>[233.675665273316 358.444268586839 79.6476923700931 169.170604055052 135.149491703846 48.4017370677397 84.0095135619193 403.182919810813 726.40294791366 564.441223627917 251.967366411464 65.8418888270228 36.8869663030241]</mn>
- <vr>[1706.21790346895;372.787079184256;635.873928235918;1953.81875117957;781.155402375773;200.746155350735;381.681592109492;16411.8647940027;2274.60437264715;12596.9622166572;4320.0517406944;758.48441243285;51.6636550746829]</vr>
- <ll>-5.67867612838745</ll>
- <Affine_translation>[-0.554216003033751 -31.0897574925538 2.65829758333071]</Affine_translation>
- <Affine_rotation>[0.0992491066590116 -0.0270415485649115 -0.0862805815400427]</Affine_rotation>
- <Affine_scaling>[1.02124645104242 1.00634608320306 1.12137744238268]</Affine_scaling>
- <Affine_shearing>[0.000200246999939311 0.00448405629399383 -0.00181697158412933]</Affine_shearing>
- <Affine0_translation>[-0.554216003033751 -31.0897574925538 2.65829758333071]</Affine0_translation>
- <Affine0_rotation>[0.0992491066590116 -0.0270415485649115 -0.0862805815400427]</Affine0_rotation>
- <Affine0_scaling>[1.02124645104242 1.00634608320306 1.12137744238268]</Affine0_scaling>
- <Affine0_shearing>[0.000200246999939311 0.00448405629399383 -0.00181697158412933]</Affine0_shearing>
- </SPMpreprocessing>
- <filedata>
- <path>/var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2</path>
- <file>sub-0026036_ses-2_run-1_T1w</file>
- <fname>/var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/sub-0026036_ses-2_run-1_T1w.nii</fname>
- <F>/var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/sub-0026036_ses-2_run-1_T1w.nii</F>
- <Fm>/var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/mri/msub-0026036_ses-2_run-1_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/mri/p0sub-0026036_ses-2_run-1_T1w.nii</Fp0>
- <fnames>../Utah_1/sub-0026036/ses-2/sub-0026036_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_3274552/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>26</SurfaceEulerNumber>
- <SurfaceDefectArea>0.527970021239944</SurfaceDefectArea>
- <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0776237100362778</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0709397196769714</SurfacePositionRMSE>
- <res_vx_vol>[1.20000000867543 0.499999987805243 0.499999992739821]</res_vx_vol>
- <res_vx_voli>[0.800000007739598 0.799999992723452 0.800000000428213]</res_vx_voli>
- <res_RMS>0.804155872404122</res_RMS>
- <res_BB>NaN</res_BB>
- <tissue_mn>[22.9489994049072 61.101001739502 207.389999389648 355.890991210938]</tissue_mn>
- <tissue_mnr>[0.0644832253456116 0.171684592962265 0.58273458480835 1]</tissue_mnr>
- <tissue_weighting>T1</tissue_weighting>
- <tissue_std>[10.9301134937118 38.0216576030693 36.9135384518705 26.4969832817446]</tissue_std>
- <tissue_stdr>[0.0328288823366165 0.114199049770832 0.110870778560638 0.0795843824744225]</tissue_stdr>
- <contrast>122.472061157227</contrast>
- <contrastr>0.344128012657166</contrastr>
- <res_ECR>0.312185108661652</res_ECR>
- <NCR>0.182298630475998</NCR>
- <ICR>0.299458205699921</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[2.40000001735087 0.999999975610486 0.999999985479643]</res_vx_vol>
- <res_RMS>1.60831174480824</res_RMS>
- <res_ECR>2.49074029922485</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>2.9214129447937</contrastr>
- <NCR>2.94801354408264</NCR>
- <ICR>1.20252537727356</ICR>
- <SurfaceEulerNumber>2.22448979591837</SurfaceEulerNumber>
- <SurfaceDefectArea>1.13199250530999</SurfaceDefectArea>
- <SurfaceDefectNumber>1.875</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>1.5524742603302</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>1.41879439353943</SurfacePositionRMSE>
- <SIQR>2.6470234639839</SIQR>
- <IQR>2.70598305540677</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>20231031-001214</date>
- </software>
- <subjectmeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <qualitymeasures>
- <software>
- <version_segment>1639</version_segment>
- </software>
- <SurfaceEulerNumber>26</SurfaceEulerNumber>
- <SurfaceDefectArea>0.527970021239944</SurfaceDefectArea>
- <SurfaceDefectNumber>17.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.0776237100362778</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.0709397196769714</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>26</EC_abs>
- <defect_size>0.527970021239944</defect_size>
- <vol_abs_CGW>[239.104267309518 877.185478749803 535.51289383582 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0.949992910862289</vol_abs_WMH>
- <vol_rel_WMH>0.000575124950110623</vol_rel_WMH>
- <surf_TSA>2216.6500055626</surf_TSA>
- <vol_TIV>1651.80263989514</vol_TIV>
- <vol_rel_CGW>[0.144753532616159 0.531047388812436 0.324199078571405 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[2.69802520775989 0.622343895851787]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[2.7081286907196 0.774587138106601 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[2.0892077978052 0.256683538010669 0.301747239210771;2.73955607925243 0.183675702963565 0.430412983813455;3.40401658370974 0.278713446074816 0.267839776975774]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.947327224243366 0.450286863292409 0.566052009456265;4.30260474330123 0.295519396930716 0.433947990543735]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>2.37037130296947</vol_TIV>
- <vol_rel_CGW>[0.5 7.38734534505094 3.67239724445771 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1.05751249501106</vol_rel_WMH>
- <surf_TSA>8.62392869016343</surf_TSA>
- <SQR>6.04392763561147</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 11796.4796262835 0.499766924585918]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.00115204893518239 0.000892971293069422 0.123760603368282]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[1032.6658260289 467.477329838454 630.462376357287 363.410079024476 972.535764910933 8962.66319304394]</SPMvols0>
- <SPMvols1>[868.373195759594 441.585168554706 313.613790216057 334.312671243039 847.233534936042 8991.45403128778]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[80.9337997436523 217.434097290039 359.807006835938]</T3th>
- <Tth>
- <T3th>[-166.595321655273 -37.4105377197266 8.14304351806641 80.9337997436523 217.434097290039 359.807006835938 499.243591308594 1036.43627929688]</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>[0.0199982430785894 0.067117765545845 0.0739816054701805 0 0]</dtc>
- <ll>[0.0834190731956845 0 0.0834190731956845 0;0.205094226411268 0.00897685677206674 0.214071083183334 1914.29675292969;0.205094226411268 0.00897685677206674 0.214071083183334 1914.29675292969]</ll>
- <rmsdtc>[0.0424544028937817 0.0905801132321358 0.101652689278126]</rmsdtc>
- <rmsgdt>[0.0300320349633694 0.0428501740098 0.0534626170992851]</rmsgdt>
- <rmsdt>0.101652689278126</rmsdt>
- <dt>0.0739816054701805</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>[0.00822710990905762 0.0286941137164831 0.040831845253706 0.0507551655173302 0.0591140240430832 0.0661489516496658]</dtc>
- <ll>[0.0811182232154662 0 0.0811182232154662 0;0.218627976190476 0.0107779456654457 0.229405921855922 5516.9609375;0.202772558676248 0.0144480888058348 0.217220647482083 10398.462890625;0.183933892028171 0.0179379925995018 0.201871884627673 19342.03515625;0.166802079826084 0.0219364405726003 0.188738520398685 38374.578125;0.166802079826084 0.0219364405726003 0.188738520398685 38374.578125]</ll>
- <rmsdtc>[0.00983038637787104 0.0343770235776901 0.053039912134409 0.0807070955634117 0.109630882740021 0.116894200444221]</rmsdtc>
- <rmsgdt>[0.0029238979332149 0.0116163250058889 0.0277181137353182 0.0511757582426071 0.0745077431201935 0.0807784125208855]</rmsgdt>
- <rmsdt>0.116894200444221</rmsdt>
- <dt>0.0661489516496658</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r2040: 1/1: ./sub-0026036/ses-2/sub-0026036_ses-2_run-1_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 211s</item>
- <item>Internal resampling (1.20x0.50x0.50mm > 0.80x0.80x0.80mm): 2s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 10s</item>
- <item>Estimate background 8s</item>
- <item>Initial correction 9s</item>
- <item>Refine background 5s</item>
- <item>Final correction 8s</item>
- <item>Final scaling 8s</item>
- <item>58s</item>
- <item>Correct center-of-mass 3s</item>
- <item>Affine registration 21s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 113s</item>
- <item>SPM preprocessing 1 (estimate 2): 37s</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 26s</item>
- <item>Update Segmentation 31s</item>
- <item>Update Skull-Stripping 73s</item>
- <item>Update probability maps 16s</item>
- <item>145s</item>
- <item>Global intensity correction: 25s</item>
- <item>SANLM denoising after intensity normalization (medium): 48s</item>
- <item>Fast Optimized Shooting registration 36s</item>
- <item>Local adaptive segmentation (LASstr=0.50):</item>
- <item>Prepare maps 6s</item>
- <item>Prepare partitions 5s</item>
- <item>Prepare segments (LASmod = 1.00) 24s</item>
- <item>Estimate local tissue thresholds (WM) 31s</item>
- <item>Estimate local tissue thresholds (GM) 45s</item>
- <item>Intensity transformation 0s</item>
- <item>SANLM denoising after LAS (medium) 62s</item>
- <item>181s</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 12s</item>
- <item>Major structures 6s</item>
- <item>Ventricle detection 20s</item>
- <item>Blood vessel detection 17s</item>
- <item>WMH detection (WMHCstr=0.50 > WMHCstr'=0.01) 38s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 3s</item>
- <item>Side alignment 6s</item>
- <item>Final corrections 7s</item>
- <item>109s</item>
- <item>Blood vessel correction (BVCstr=0.50): 3s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.06): 53s</item>
- <item>AMAP peaks: [CSF,GM,WM] = [0.36 0.05,0.68 0.08,0.98 0.05]</item>
- <item>Final cleanup (gcutstr=0.25):</item>
- <item>Level 1 cleanup (ROI estimation) 7s</item>
- <item>Level 1 cleanup (brain masking) 4s</item>
- <item>Level 2 cleanup (CSF correction) 2s</item>
- <item>Level 3 cleanup (CSF/WM PVE) 5s</item>
- <item>18s</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 | 0.0811 0.0000 0.0811 | 32.0000</item>
- <item>2 | 2.50 | 0.0792 0.0009 0.0802 | 29.4886</item>
- <item>3 | 2.50 | 0.0787 0.0014 0.0801 | 26.9772</item>
- <item>4 | 2.50 | 0.0784 0.0016 0.0800 | 24.6107</item>
- <item>5 | 2.50 | 0.0782 0.0017 0.0799 | 22.6548</item>
- <item>6 | 2.50 | 0.0780 0.0018 0.0798 | 20.6989</item>
- <item>7 | 2.50 | 0.0778 0.0018 0.0796 | 18.9688</item>
- <item>8 | 2.50 | 0.0776 0.0019 0.0795 | 17.4455</item>
- <item>9 | 2.50 | 0.0774 0.0020 0.0793 | 15.9223</item>
- <item>10 | 2.50 | 0.0771 0.0021 0.0792 | 14.6627</item>
- <item>11 | 2.50 | 0.0769 0.0021 0.0790 | 13.4764</item>
- <item>12 | 2.50 | 0.0767 0.0022 0.0788 | 12.3015</item>
- <item>13 | 2.50 | 0.0764 0.0022 0.0787 | 11.3776</item>
- <item>14 | 2.50 | 0.0762 0.0023 0.0785 | 10.4537</item>
- <item>15 | 2.25 | 0.0755 0.0023 0.0778 | 9.5920</item>
- <item>16 | 2.25 | 0.0729 0.0036 0.0765 | 8.8725</item>
- <item>29 | 2.00 | 0.0749 0.0016 0.0765 | 3.3283</item>
- <item>30 | 2.00 | 0.0693 0.0039 0.0733 | 3.1221</item>
- <item>31 | 2.00 | 0.0676 0.0048 0.0724 | 2.9160</item>
- <item>43 | 1.75 | 0.0672 0.0027 0.0700 | 1.5785</item>
- <item>44 | 1.75 | 0.0628 0.0052 0.0679 | 1.5194</item>
- <item>45 | 1.75 | 0.0613 0.0060 0.0673 | 1.4626</item>
- <item>57 | 1.50 | 0.0602 0.0043 0.0645 | 1.0900</item>
- <item>58 | 1.50 | 0.0567 0.0066 0.0633 | 1.0730</item>
- <item>59 | 1.50 | 0.0556 0.0073 0.0629 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 125s</item>
- <item>Prepare output 12s</item>
- <item>136s</item>
- <item>Jacobian determinant (RMS): 0.010 0.034 0.053 0.081 0.110 | 0.116894</item>
- <item>Template Matching: 0.081 0.219 0.203 0.184 0.167 | 0.166802</item>
- <item>Write result maps: 183s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 27s</item>
- <item>CSF distance: 14s</item>
- <item>PBT2x thickness: 39s</item>
- <item>85s</item>
- <item>Create initial surface 70s</item>
- <item>Topology correction: 81s</item>
- <item>Surface refinement: 89s</item>
- <item>Reduction of surface collisions with optimization: 66s</item>
- <item>Spherical mapping with areal smoothing 132s</item>
- <item>Spherical registration 252s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 29s</item>
- <item>CSF distance: 16s</item>
- <item>PBT2x thickness: 42s</item>
- <item>93s</item>
- <item>Create initial surface 73s</item>
- <item>Topology correction: 77s</item>
- <item>Surface refinement: 74s</item>
- <item>Reduction of surface collisions with optimization: 74s</item>
- <item>Spherical mapping with areal smoothing 72s</item>
- <item>Spherical registration 214s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 2.6980 0.6223 mm</item>
- <item>Surface intensity / position RMSE: 0.0776 / 0.0709</item>
- <item>Euler number / defect number / defect size: 26.0 / 17.5 / 0.53%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/surf/lh.thickness.sub-0026036_ses-2_run-1_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/surf/rh.thickness.sub-0026036_ses-2_run-1_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/sub-0026036_ses-2_run-1_T1w.nii</item>
- <item>Surface ROI estimation: 9s</item>
- <item>Surface and thickness estimation takes: 1588s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 17s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 60s</item>
- <item>ROI estimation of 'lpba40' atlas 16s</item>
- <item>ROI estimation of 'hammers' atlas 36s</item>
- <item>ROI estimation of 'thalamus' atlas 3s</item>
- <item>ROI estimation of 'ibsr' atlas 13s</item>
- <item>ROI estimation of 'aal3' atlas 21s</item>
- <item>ROI estimation of 'mori' atlas 32s</item>
- <item>ROI estimation of 'anatomy3' atlas 46s</item>
- <item>ROI estimation of 'julichbrain' atlas 59s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 24s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 46s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 98s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 146s</item>
- <item>ROI estimation of 'Tian_Subcortex_S2_7T' atlas 14s</item>
- <item>Write results 15s</item>
- <item>631s</item>
- <item>Quality check: 42s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/report/catreport_sub-0026036_ses-2_run-1_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 62 minute(s) and 23 second(s).</item>
- <item>Image Quality Rating (IQR): 77.94% (C+)</item>
- <item>GM volume (GMV): 53.10% (877.19 / 1651.80 ml)</item>
- <item>GM thickness (GMT): 2.70 0.62 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_3274552/ds/Utah_1/sub-0026036/ses-2/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
|