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ds000007-catqc/sub-03/report/cat_sub-03_T1w.xml
Felix Hoffstaedter 49a1686fa7 [DATALAD RUNCMD] Compute CAT12.9 QC for sub-03 
=== Do not change lines below ===
{
 "chain": [],
 "cmd": "singularity exec -B {pwd} --cleanenv code/cat12/cat12.9_r2665.simg sh -e -u -x -c '\n        mkdir -p {outputs[0]} || true         && cp {inputs[0]} {outputs[0]}         && /singularity -b /batch/CATpreprocessing4qc+ROIs.m {outputs[0]}/*.nii.gz         && rm -f {outputs[0]}/*.nii* {outputs[0]}/report/*.jpg         && gzip {outputs[0]}/*/*.nii         '",
 "dsid": "a4334989-99d1-47ac-9d97-91726e2296e4",
 "exit": 0,
 "extra_inputs": [
  "code/cat12/cat12.9_r2665.simg"
 ],
 "inputs": [
  "sourcedata/raw/sub-03/anat/sub-03_T1w.nii.gz"
 ],
 "outputs": [
  "sub-03"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^
2025-10-14 18:44:49 +02:00

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<?xml version="1.0" encoding="utf-8"?>
<S>
<SPMpreprocessing>
<Affine>[1.10418464414711 -0.0814115511140791 -0.0159531783487877 -6.48174801734822;0.0611741926205706 0.958849677194253 0.392739506143678 -7.61900711168231;-0.00774822124468715 -0.317246448092858 1.07018598289354 -6.29627131346133;0 0 0 1]</Affine>
<Affine0>[1.10418464414711 -0.0814115511140791 -0.0159531783487877 -6.48174801734822;0.0611741926205706 0.958849677194253 0.392739506143678 -7.61900711168231;-0.00774822124468715 -0.317246448092858 1.07018598289354 -6.29627131346133;0 0 0 1]</Affine0>
<lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
<mn>[217.405863971518 328.265355896427 58.0829461824516 140.744444193246 103.630768149314 27.0215731318869 55.5453102733756 226.001847441243 315.81505196516 373.993826296499 188.117849033694 105.04274143922 19.4660691186206]</mn>
<vr>[1761.05025452404;336.413356633259;631.405666567082;1094.29319171951;923.928177526488;134.806280246665;370.611167017967;1842.65613809268;29480.0426917575;7753.0860902488;688.295133634265;2998.10432595052;89.6606294283066]</vr>
<ll>-5.43515682220459</ll>
<Affine_translation>[-6.48174801734822 -7.61900711168231 -6.29627131346133]</Affine_translation>
<Affine_rotation>[0.318662287078251 -0.0106930204512749 -0.0547534709090297]</Affine_rotation>
<Affine_scaling>[1.10590507962732 1.01291099388376 1.13945721462439]</Affine_scaling>
<Affine_shearing>[-0.0235305161282741 -0.00153861819658032 0.037349282187615]</Affine_shearing>
<Affine0_translation>[-6.48174801734822 -7.61900711168231 -6.29627131346133]</Affine0_translation>
<Affine0_rotation>[0.318662287078251 -0.0106930204512749 -0.0547534709090297]</Affine0_rotation>
<Affine0_scaling>[1.10590507962732 1.01291099388376 1.13945721462439]</Affine0_scaling>
<Affine0_shearing>[-0.0235305161282741 -0.00153861819658032 0.037349282187615]</Affine0_shearing>
</SPMpreprocessing>
<filedata>
<help>Structure directory and file names. \n logdir .. path for log file \n rawdir .. origin directory of the RAW data \n BIDSfolder .. relative path to the main result directory \n BIDSdir .. absolution (full) path to the result directory \n</help>
<rawdir>/var/lib/condor/execute/dir_3982995/ds/sub-03</rawdir>
<path>/var/lib/condor/execute/dir_3982995/ds/sub-03</path>
<file>sub-03_T1w</file>
<fname>/var/lib/condor/execute/dir_3982995/ds/sub-03/sub-03_T1w.nii</fname>
<F>/var/lib/condor/execute/dir_3982995/ds/sub-03/sub-03_T1w.nii</F>
<Fm>/var/lib/condor/execute/dir_3982995/ds/sub-03/mri/msub-03_T1w.nii</Fm>
<Fp0>/var/lib/condor/execute/dir_3982995/ds/sub-03/mri/p0sub-03_T1w.nii</Fp0>
<fnames>..ute/dir_3982995/ds/sub-03/sub-03_T1w</fnames>
</filedata>
<parameter>
<opts>
<tpm>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/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>
<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/CAT12.9_2665</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/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym</pth_templates>
<darteltpm>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
</darteltpm>
<shootingtpm>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
</shootingtpm>
<shootingT1>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_T1_masked.nii</item>
</shootingT1>
<brainmask>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/brainmask.nii</item>
</brainmask>
<T1>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/T1.nii</item>
</T1>
<cat12atlas>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/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>1</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/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/neuromorphometrics.nii</td>
<td>0</td>
<td>
<item>csf</item>
<item>gm</item>
<item>wm</item>
</td>
<td>1</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/lpba40.nii</td>
<td>0</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>1</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cobra.nii</td>
<td>0</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>1</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/hammers.nii</td>
<td>0</td>
<td>
<item>csf</item>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamus.nii</td>
<td>0</td>
<td>
<item>gm</item>
</td>
<td>1</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/thalamic_nuclei.nii</td>
<td>0</td>
<td>
<item>gm</item>
</td>
<td>1</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/suit.nii</td>
<td>0</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>1</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/ibsr.nii</td>
<td>0</td>
<td>
<item>csf</item>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/aal3.nii</td>
<td>1</td>
<td>
<item>gm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/mori.nii</td>
<td>1</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/anatomy3.nii</td>
<td>1</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/julichbrain.nii</td>
<td>1</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Tian_Subcortex_S4_7T.nii</td>
<td>1</td>
<td>
<item>gm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_100Parcels_17Networks_order.nii</td>
<td>1</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_200Parcels_17Networks_order.nii</td>
<td>1</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_400Parcels_17Networks_order.nii</td>
<td>1</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
<tr>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Schaefer2018_600Parcels_17Networks_order.nii</td>
<td>1</td>
<td>
<item>gm</item>
<item>wm</item>
</td>
<td>0</td>
</tr>
</atlas>
<satlas>
<tr>
<td>Desikan</td>
<td>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/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/spm25_mcr/home/ubuntu/Desktop/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/spm25_mcr/home/ubuntu/Desktop/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/spm25_mcr/home/ubuntu/Desktop/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/spm25_mcr/home/ubuntu/Desktop/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/spm25_mcr/home/ubuntu/Desktop/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/spm25_mcr/home/ubuntu/Desktop/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/spm25_mcr/home/ubuntu/Desktop/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>
<WMHtpm>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat_wmh_miccai2017.nii</item>
</WMHtpm>
<BVtpm>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat_bloodvessels.nii</item>
</BVtpm>
<SLtpm>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/cat_strokelesions_ATLAS303.nii</item>
</SLtpm>
<pbtmethod>pbtsimple</pbtmethod>
<darteltpms>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_Dartel.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_Dartel.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_Dartel.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_Dartel.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_5_Dartel.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
</darteltpms>
<shootingtpms>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
</shootingtpms>
<templates>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_1_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_2_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_3_GS.nii</item>
<item>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_4_GS.nii</item>
</templates>
<inv_weighting>0</inv_weighting>
<AMAPframing>1</AMAPframing>
</extopts>
</parameter>
<qualitymeasures>
<res_vx_vol>[1 1.33333337306976 1.33333337306976]</res_vx_vol>
<res_vx_voli>[1 1 1]</res_vx_voli>
<res_RMS>1.2322818627088</res_RMS>
<res_BB>0</res_BB>
<FEC>355.220751528387</FEC>
<res_ECR>0.486046314239502</res_ECR>
<tissue_mn>[0 103.535003662109 258.628601074219 375.522186279297]</tissue_mn>
<tissue_mnr>[0 0.275709420442581 0.688717246055603 1]</tissue_mnr>
<tissue_weighting>T1</tissue_weighting>
<tissue_std>[0.378804353098143 0.0800855427604814 0.0859036091875635 0.0601951142325488]</tissue_std>
<tissue_stdr>[0.00100874027702957 0.000213264473131858 0.000228757751756348 0.000160297087859362]</tissue_stdr>
<contrast>103.535003662109</contrast>
<contrastr>0.275709420442581</contrastr>
<NCR>0.111390850889739</NCR>
<ICR>0.325667172670364</ICR>
</qualitymeasures>
<qualityratings>
<res_vx_vol>[2 2.66666674613953 2.66666674613953]</res_vx_vol>
<res_RMS>2.46456372541759</res_RMS>
<res_ECR>3.0631217956543</res_ECR>
<res_BB>1</res_BB>
<tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
<tissue_std>[5.73863091259201 1.03770108298413 1.01891339592342 1.14951063390774]</tissue_std>
<contrast>-1547.02502441406</contrast>
<contrastr>1.86435866355896</contrastr>
<NCR>1.93010121862962</NCR>
<ICR>1.26752769947052</ICR>
<FEC>3.55220751528387</FEC>
<SIQR>2.784564856817</SIQR>
<IQR>2.24465155159267</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>
<FEC>quick Euler characteristic</FEC>
</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>
</subjectmeasures>
</ratings_help>
<software>
<version_segment>1639</version_segment>
<system>LINUX</system>
<version_spm>25.01.02</version_spm>
<version_matlab>23.2</version_matlab>
<version_cat>12.9</version_cat>
<revision_cat>2665</revision_cat>
<function>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_vol_qa202205.m</function>
<markdefs>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_stat_marks.m</markdefs>
<qamethod>cat12</qamethod>
<date>20251014-184344</date>
</software>
<subjectmeasures>
<software>
<version_segment>1639</version_segment>
</software>
<vol_abs_CGW>[183.041847058824 753.071996078431 540.046623529412 0 0]</vol_abs_CGW>
<vol_abs_WMH>0.638866666666667</vol_abs_WMH>
<vol_rel_WMH>0.000432789443351845</vol_rel_WMH>
<vol_TIV>1476.16046666667</vol_TIV>
<vol_rel_CGW>[0.123998610714831 0.510155916706638 0.365845472578531 0 0]</vol_rel_CGW>
</subjectmeasures>
<subjectratings>
<vol_TIV>1.13694997941547</vol_TIV>
<vol_rel_CGW>[0.0768428648496978 7.01213930866806 4.42035690694201 -2.15014367816092 -2.15014367816092]</vol_rel_CGW>
<vol_rel_WMH>1.04327894433518</vol_rel_WMH>
<SQR>3.94871607913931</SQR>
</subjectratings>
<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>
<FEC>quick Euler characteristic</FEC>
</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>
</subjectmeasures>
</help>
<ppe>
<affreg>
<skullstrippedBGth>9.07528638839722</skullstrippedBGth>
<skullstrippedpara>[0 1 0 10485.760625 0.436699764807217]</skullstrippedpara>
<skullstripped>[false]</skullstripped>
<highBGpara>[0.0290031116455793 0.0295959785580635 0.0997872203588486]</highBGpara>
<highBG>[false]</highBG>
<Affine_catfinal>[1.13634036004752 -0.0721364536926105 -0.0219219644710215 -6.79842614707971;0.0499195699520842 0.948712498978986 0.377774457469292 -6.87566282358107;-0.00552883412521495 -0.316176860177759 1.04412521076537 -5.17542827101199;0 0 0 1]</Affine_catfinal>
</affreg>
<SPMvols0>[904.663039215686 466.702847058824 366.667482352941 650.138 1370.93920392157 7443.39285490196]</SPMvols0>
<SPMvols1>[786.573623529412 434.596960784314 198.696501960784 820.157670588235 885.814654901961 7360.62722352941]</SPMvols1>
<tths>
<gintnorm>
<T3th>[52.13330078125 202.867706298828 329.154205322266]</T3th>
<Tth>
<T3th>[-132.520355224609 -45.2755737304688 3.42886352539062 52.13330078125 202.867706298828 329.154205322266 467.664672851562 992.555053710938]</T3th>
<T3thx>[0 0.02 0.05 1 2 3 4 5]</T3thx>
</Tth>
</gintnorm>
</tths>
<reginitp>
<opt>
<nits>8</nits>
<vxreg>1.5</vxreg>
<rres>1.5</rres>
<stepsize>0.5</stepsize>
<resfac>[2 1.66666666666667 1.33333333333333 1 1]</resfac>
<ll1th>0.0075</ll1th>
<ll3th>[0.015 0.015 0.015 0.015 0.015;0.015 0.015 0.015 0.015 0.015;0.015 0.015 0.015 0.015 0.015;0.015 0.015 0.015 0.015 0.015;0.015 0.015 0.015 0.015 0.015]</ll3th>
<regstr>12</regstr>
</opt>
<fast>0</fast>
<clsn>2</clsn>
<regra>1</regra>
<testfolder>Shooting_Template_0_GS_tr1.5_rr3.0-1.5_or1.5_regstr12.0</testfolder>
<dtc>[0.0163286756724119 0.0241801273077726 0.031306941062212 0.0484526380896568 0.0547010488808155 0.0547010488808155]</dtc>
<ll>[0.0772374379439276 0 0.0772374379439276 0;0.0726940130979612 0.00112071878262831 0.0738147318805895 1237.60302734375;0.0713558426842959 0.00131256217493508 0.072668404859231 2834.00024414062;0.0634420804434554 0.00233841662936716 0.0657804970728225 12272.1484375;0.0581240309512526 0.00404628279891194 0.0621703137501646 21235.130859375;0.174372092853758 0.0121388483967358 0.186510941250494 21235.130859375]</ll>
<rmsdtc>[0.0445316396653652 0.0311226304620504 0.0447151400148869 0.0831625685095787 0.098158948123455 0.098158948123455]</rmsdtc>
<rmsgdt>[0.0331096686422825 0.0129774007946253 0.0248788595199585 0.0579119101166725 0.0727740302681923 0.0727740302681923]</rmsgdt>
<rmsdt>0.098158948123455</rmsdt>
<dt>0.0547010488808155</dt>
</reginitp>
<Affine_SPMfinal>[1.1064626647925 -0.0796365937825961 -0.0200028285143822 -6.67319862136865;0.0587921645106232 0.957414628736201 0.384861088332591 -6.7704652028863;-0.00564405250045719 -0.319928930711826 1.09971627351466 -6.47799382177185;0 0 0 1]</Affine_SPMfinal>
<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>[0.00672355014830828 0.0221438072621822 0.0330875366926193 0.0425489209592342 0.0497719198465347 0.0546905696392059]</dtc>
<ll>[0.077429865540789 0 0.077429865540789 0;0.210361324786325 0.00869772111568987 0.219059045902015 4452.14599609375;0.195107535201581 0.0135575741798455 0.208665109381426 9757.548828125;0.175865702253235 0.0169514894259055 0.19281719167914 18278.31640625;0.159388392451381 0.0200860845945615 0.179474477045942 35137.65234375;0.159388392451381 0.0200860845945615 0.179474477045942 35137.65234375]</ll>
<rmsdtc>[0.00817706529051065 0.0279065258800983 0.044555738568306 0.0688569843769073 0.092291995882988 0.0986030101776123]</rmsdtc>
<rmsgdt>[0.00281518627889454 0.0108091430738568 0.0251476746052504 0.0453823618590832 0.0642173439264297 0.0697110742330551]</rmsgdt>
<rmsdt>0.0986030101776123</rmsdt>
<dt>0.0546905696392059</dt>
</reg>
</ppe>
<catlog>
<item>------------------------------------------------------------------------</item>
<item>CAT12.9 r2665: 1/1: ./condor/execute/dir_3982995/ds/sub-03/sub-03_T1w.n</item>
<item>------------------------------------------------------------------------</item>
<item>SANLM denoising (medium) 51s</item>
<item>Internal resampling (1.00x1.33x1.33mm &gt; 1.00x1.00x1.00mm) 1s</item>
<item>Affine preprocessing (APP)</item>
<item>Initialize 8s</item>
<item>Estimate background 9s</item>
<item>Initial correction 6s</item>
<item>Refine background 4s</item>
<item>Final correction 5s</item>
<item>Final scaling 6s</item>
<item>45s</item>
<item>Correct center-of-mass 4s</item>
<item>Affine registration 8s</item>
<item>SPM preprocessing 1 (estimate 1 - TPM registration): 87s</item>
<item>SPM preprocessing 1 (estimate 2): 73s</item>
<item>SPM preprocessing 2 (write)</item>
<item>Write Segmentation 19s</item>
<item>Update Segmentation 17s</item>
<item>Update Skull-Stripping 44s</item>
<item>Update probability maps 8s</item>
<item>88s</item>
<item>Global intensity correction 16s</item>
<item>SANLM denoising after intensity normalization (medium) 21s</item>
<item>Fast Optimized Shooting registration 3s</item>
<item>119s</item>
<item>Local adaptive segmentation (LASstr=0.50)</item>
<item>Prepare maps 5s</item>
<item>Prepare partitions 2s</item>
<item>Prepare segments (LASmod = 1.01) 16s</item>
<item>Estimate local tissue thresholds (WM) 20s</item>
<item>Estimate local tissue thresholds (GM) 24s</item>
<item>Intensity transformation 0s</item>
<item>SANLM denoising after LAS (medium) 38s</item>
<item>107s</item>
<item>ROI segmentation (partitioning)</item>
<item>Atlas -&gt; subject space 10s</item>
<item>Major structures 21s</item>
<item>Ventricle detection 19s</item>
<item>Blood vessel detection 10s</item>
<item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 90s</item>
<item>Manual stroke lesion detection 0s</item>
<item>Closing of deep structures 2s</item>
<item>Side alignment 5s</item>
<item>Final corrections 3s</item>
<item>160s</item>
<item>Apply enhanced blood vessel correction 1s</item>
<item>Amap using initial SPM12 segmentations (MRF filter strength 0.06) 31s</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) 5s</item>
<item>Level 1 cleanup (brain masking) 4s</item>
<item>Level 2 cleanup (CSF correction) 2s</item>
<item>Level 3 cleanup (CSF/WM PVE) 3s</item>
<item>13s</item>
<item>5s</item>
<item>Write result maps 2s</item>
<item>ROI estimation in native space</item>
<item>ROI estimation of 'thalamic_nuclei' atlas 3s</item>
<item>ROI estimation of 'cobra' atlas 13s</item>
<item>ROI estimation of 'neuromorphometrics' atlas 47s</item>
<item>ROI estimation of 'lpba40' atlas 13s</item>
<item>ROI estimation of 'hammers' atlas 33s</item>
<item>ROI estimation of 'thalamus' atlas 2s</item>
<item>ROI estimation of 'suit' atlas 7s</item>
<item>ROI estimation of 'ibsr' atlas 11s</item>
<item>ROI estimation of 'aal3' atlas 19s</item>
<item>ROI estimation of 'mori' atlas 16s</item>
<item>ROI estimation of 'anatomy3' atlas 24s</item>
<item>ROI estimation of 'julichbrain' atlas 31s</item>
<item>ROI estimation of 'Tian_Subcortex_S4_7T' atlas 7s</item>
<item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 13s</item>
<item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 25s</item>
<item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 88s</item>
<item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 84s</item>
<item>Write results 86s</item>
<item>441s</item>
<item>Quality check 12s</item>
<item>/var/lib/condor/execute/dir_3982995/ds/sub-03/report/catreport_sub-03_T1w.pdf</item>
<item>------------------------------------------------------------------------</item>
<item>CAT preprocessing takes 26 minute(s) and 25 second(s).</item>
<item>Image Quality Rating (IQR): 82.55% (B-)</item>
<item>GM volume (GMV): 51.02% (753.07 / 1476.16 ml)</item>
<item>Segmentations are saved in /var/lib/condor/execute/dir_3982995/ds/sub-03/mri</item>
<item>Reports are saved in /var/lib/condor/execute/dir_3982995/ds/sub-03/report</item>
<item>Labels are saved in /var/lib/condor/execute/dir_3982995/ds/sub-03/label</item>
<item>------------------------------------------------------------------------</item>
</catlog>
</S>
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