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ds000007-catqc/sub-12/report/cat_sub-12_T1w.xml
Felix Hoffstaedter 54df6f7c7c [DATALAD RUNCMD] Compute CAT12.9 QC for sub-12 
=== 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-12/anat/sub-12_T1w.nii.gz"
 ],
 "outputs": [
  "sub-12"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^
2025-10-14 18:35:34 +02:00

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<?xml version="1.0" encoding="utf-8"?>
<S>
<SPMpreprocessing>
<Affine>[1.06761460551346 0.0538078031498554 -0.0302895625247165 0.931660149621047;-0.0127306609789532 0.941552188041888 0.383478769990804 8.9502713138559;0.0436299480261507 -0.378261719591399 1.05997369036043 3.54137567936077;0 0 0 1]</Affine>
<Affine0>[1.06761460551346 0.0538078031498554 -0.0302895625247165 0.931660149621047;-0.0127306609789532 0.941552188041888 0.383478769990804 8.9502713138559;0.0436299480261507 -0.378261719591399 1.05997369036043 3.54137567936077;0 0 0 1]</Affine0>
<lkp>[1 2 3 3 4 4 4 5 5 5 5 6 6]</lkp>
<mn>[220.55397981362 341.396919479798 66.5111804951669 140.498741703417 106.781619832195 26.1453911771777 57.8873684259864 247.357878755083 326.590157008494 392.479254108693 191.622256738612 131.616724315766 25.5512810839867]</mn>
<vr>[2040.44619973151;441.470725195174;629.95484261855;1213.5674782608;1628.00661581383;121.043618578951;504.971357541629;2506.17105240705;33324.8858347196;9218.10890507704;1136.95800446623;2160.80948889077;252.654133801243]</vr>
<ll>-5.52537250518799</ll>
<Affine_translation>[0.931660149621047 8.9502713138559 3.54137567936077]</Affine_translation>
<Affine_rotation>[0.383780503177048 -0.0334166561702479 0.0263378430003996]</Affine_rotation>
<Affine_scaling>[1.06858157760621 1.01575757795826 1.12683522227283]</Affine_scaling>
<Affine_shearing>[0.0253583702086449 0.00790554654545897 -0.0404559033712081]</Affine_shearing>
<Affine0_translation>[0.931660149621047 8.9502713138559 3.54137567936077]</Affine0_translation>
<Affine0_rotation>[0.383780503177048 -0.0334166561702479 0.0263378430003996]</Affine0_rotation>
<Affine0_scaling>[1.06858157760621 1.01575757795826 1.12683522227283]</Affine0_scaling>
<Affine0_shearing>[0.0253583702086449 0.00790554654545897 -0.0404559033712081]</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_1648529/ds/sub-12</rawdir>
<path>/var/lib/condor/execute/dir_1648529/ds/sub-12</path>
<file>sub-12_T1w</file>
<fname>/var/lib/condor/execute/dir_1648529/ds/sub-12/sub-12_T1w.nii</fname>
<F>/var/lib/condor/execute/dir_1648529/ds/sub-12/sub-12_T1w.nii</F>
<Fm>/var/lib/condor/execute/dir_1648529/ds/sub-12/mri/msub-12_T1w.nii</Fm>
<Fp0>/var/lib/condor/execute/dir_1648529/ds/sub-12/mri/p0sub-12_T1w.nii</Fp0>
<fnames>..ute/dir_1648529/ds/sub-12/sub-12_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>406.612587859778</FEC>
<res_ECR>0.506539344787598</res_ECR>
<tissue_mn>[0 119.572631835938 272.844421386719 396.397857666016]</tissue_mn>
<tissue_mnr>[0 0.301648020744324 0.688309550285339 1]</tissue_mnr>
<tissue_weighting>T1</tissue_weighting>
<tissue_std>[0.373875070315759 0.0850832665975166 0.0901128951498661 0.0603980545538508]</tissue_std>
<tissue_stdr>[0.000943181337788701 0.000214641084312461 0.000227329423069023 0.000152367254486308]</tissue_stdr>
<contrast>119.572631835938</contrast>
<contrastr>0.301648020744324</contrastr>
<NCR>0.11364688203159</NCR>
<ICR>0.322719514369965</ICR>
</qualitymeasures>
<qualityratings>
<res_vx_vol>[2 2.66666674613953 2.66666674613953]</res_vx_vol>
<res_RMS>2.46456372541759</res_RMS>
<res_ECR>3.18022489547729</res_ECR>
<res_BB>1</res_BB>
<tissue_mn>[1.89584374427795 8.62400054931641 8.62400054931641 8.62400054931641]</tissue_mn>
<tissue_std>[5.63868060955066 1.02117563933648 1.00931034699251 1.14800485401879]</tissue_std>
<contrast>-1787.58947753906</contrast>
<contrastr>1.47527968883514</contrastr>
<NCR>1.96248753993095</NCR>
<ICR>1.26021707057953</ICR>
<FEC>4.06612587859778</FEC>
<SIQR>3.04506997494288</SIQR>
<IQR>2.25513488011934</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>20251014-183438</date>
</software>
<subjectmeasures>
<software>
<version_segment>1639</version_segment>
</software>
<vol_abs_CGW>[186.643388235294 753.426180392157 542.770450980392 0 0]</vol_abs_CGW>
<vol_abs_WMH>0.634533333333333</vol_abs_WMH>
<vol_rel_WMH>0.000427917593902776</vol_rel_WMH>
<vol_TIV>1482.84001960784</vol_TIV>
<vol_rel_CGW>[0.12586886364495 0.508096740329014 0.366034396026036 0 0]</vol_rel_CGW>
</subjectmeasures>
<subjectratings>
<vol_TIV>1.16175765716075</vol_TIV>
<vol_rel_CGW>[0.110432177531424 6.97515697429983 4.42374992862852 -2.15014367816092 -2.15014367816092]</vol_rel_CGW>
<vol_rel_WMH>1.04279175939028</vol_rel_WMH>
<SQR>3.93651645967521</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>9.27480602264404</skullstrippedBGth>
<skullstrippedpara>[0 1 0 10485.760625 0.465260777385503]</skullstrippedpara>
<skullstripped>[false]</skullstripped>
<highBGpara>[0.0287009030580521 0.0292582958936691 0.104906395077705]</highBGpara>
<highBG>[false]</highBG>
<Affine_catfinal>[1.05805983209308 0.0647659097129094 -0.048016746970474 1.03372837833931;-0.0110320266420765 0.938044439157286 0.445957628773263 11.0903434178991;0.0394278999309282 -0.427859590234868 1.05724465538879 2.69343074204057;0 0 0 1]</Affine_catfinal>
</affreg>
<SPMvols0>[934.20048627451 463.841521568627 352.094270588235 720.538796078431 1225.19722745098 7557.4944627451]</SPMvols0>
<SPMvols1>[806.7228 429.99622745098 191.702243137255 947.652282352941 856.021403921569 7255.03912156863]</SPMvols1>
<tths>
<gintnorm>
<T3th>[57.8492012023926 205.175399780273 342.760986328125]</T3th>
<Tth>
<T3th>[-126.492309570312 -28.3334045410156 11.4401006698608 57.8492012023926 205.175399780273 342.760986328125 485.216857910156 1091.25183105469]</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>[0.0149005921557546 0.0234493464231491 0.0302006248384714 0.0483053363859653 0.05537049472332 0.05537049472332]</dtc>
<ll>[0.0777506925621811 0 0.0777506925621811 0;0.0746506506645875 0.00108486906955654 0.0757355197341441 1198.01440429688;0.0732832267745061 0.00134807951500913 0.0746313062895152 2910.68701171875;0.0661856245328035 0.00234749476246837 0.0685331192952718 12319.791015625;0.0606907953969267 0.00415657394714884 0.0648473693440756 21813.9453125;0.18207238619078 0.0124697218414465 0.194542108032227 21813.9453125]</ll>
<rmsdtc>[0.038984689861536 0.0299872104078531 0.0433672219514847 0.0853564515709877 0.102867655456066 0.102867655456066]</rmsdtc>
<rmsgdt>[0.0290377736091614 0.0129593601450324 0.0255120787769556 0.0622387863695621 0.0790511220693588 0.0790511220693588]</rmsgdt>
<rmsdt>0.102867655456066</rmsdt>
<dt>0.05537049472332</dt>
</reginitp>
<Affine_SPMfinal>[1.06671351543695 0.0560087549450308 -0.0367170269036167 0.812271522107531;0.00321049807440372 0.961198037815218 0.362051218338189 10.1921451698766;0.0370214280176126 -0.399826210820938 1.10930328890582 4.5104660239408;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>[0.00689107785001397 0.0234187226742506 0.0340406000614166 0.0421694926917553 0.0491952151060104 0.0543133243918419]</dtc>
<ll>[0.0803634989300857 0 0.0803634989300857 0;0.218007219169719 0.0103592185592186 0.228366437728938 5302.625;0.203070030095371 0.0141774103304516 0.217247440425823 10203.65234375;0.183893288868671 0.0174587517835249 0.201352040652196 18825.283203125;0.167428275625331 0.0210601255149761 0.188488401140307 36841.59375;0.167428275625331 0.0210601255149761 0.188488401140307 36841.59375]</ll>
<rmsdtc>[0.00842274259775877 0.0290634483098984 0.0447724349796772 0.0685974210500717 0.0933224558830261 0.100360833108425]</rmsdtc>
<rmsgdt>[0.00277351145632565 0.0107411919161677 0.024958610534668 0.046089980751276 0.0663316920399666 0.0719777345657349]</rmsgdt>
<rmsdt>0.100360833108425</rmsdt>
<dt>0.0543133243918419</dt>
</reg>
</ppe>
<catlog>
<item>------------------------------------------------------------------------</item>
<item>CAT12.9 r2665: 1/1: ./condor/execute/dir_1648529/ds/sub-12/sub-12_T1w.n</item>
<item>------------------------------------------------------------------------</item>
<item>SANLM denoising (medium) 45s</item>
<item>Internal resampling (1.00x1.33x1.33mm &gt; 1.00x1.00x1.00mm) 1s</item>
<item>Affine preprocessing (APP)</item>
<item>Initialize 6s</item>
<item>Estimate background 7s</item>
<item>Initial correction 5s</item>
<item>Refine background 3s</item>
<item>Final correction 4s</item>
<item>Final scaling 4s</item>
<item>35s</item>
<item>Correct center-of-mass 4s</item>
<item>Affine registration 7s</item>
<item>SPM preprocessing 1 (estimate 1 - TPM registration): 70s</item>
<item>SPM preprocessing 1 (estimate 2): 49s</item>
<item>SPM preprocessing 2 (write)</item>
<item>Write Segmentation 16s</item>
<item>Update Segmentation 14s</item>
<item>Update Skull-Stripping 37s</item>
<item>Update probability maps 7s</item>
<item>74s</item>
<item>Global intensity correction 13s</item>
<item>SANLM denoising after intensity normalization (medium) 18s</item>
<item>Fast Optimized Shooting registration 7s</item>
<item>92s</item>
<item>Local adaptive segmentation (LASstr=0.50)</item>
<item>Prepare maps 4s</item>
<item>Prepare partitions 3s</item>
<item>Prepare segments (LASmod = 1.04) 14s</item>
<item>Estimate local tissue thresholds (WM) 17s</item>
<item>Estimate local tissue thresholds (GM) 22s</item>
<item>Intensity transformation 0s</item>
<item>SANLM denoising after LAS (medium) 37s</item>
<item>99s</item>
<item>ROI segmentation (partitioning)</item>
<item>Atlas -&gt; subject space 7s</item>
<item>Major structures 18s</item>
<item>Ventricle detection 21s</item>
<item>Blood vessel detection 9s</item>
<item>WMH detection (WMHCstr=0.50 &gt; WMHCstr'=0.00) 66s</item>
<item>Manual stroke lesion detection 0s</item>
<item>Closing of deep structures 1s</item>
<item>Side alignment 4s</item>
<item>Final corrections 2s</item>
<item>128s</item>
<item>Apply enhanced blood vessel correction 1s</item>
<item>Amap using initial SPM12 segmentations (MRF filter strength 0.06) 30s</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) 4s</item>
<item>Level 1 cleanup (brain masking) 3s</item>
<item>Level 2 cleanup (CSF correction) 2s</item>
<item>Level 3 cleanup (CSF/WM PVE) 3s</item>
<item>12s</item>
<item>12s</item>
<item>Write result maps 2s</item>
<item>ROI estimation in native space</item>
<item>ROI estimation of 'thalamic_nuclei' atlas 2s</item>
<item>ROI estimation of 'cobra' atlas 6s</item>
<item>ROI estimation of 'neuromorphometrics' atlas 22s</item>
<item>ROI estimation of 'lpba40' atlas 6s</item>
<item>ROI estimation of 'hammers' atlas 15s</item>
<item>ROI estimation of 'thalamus' atlas 1s</item>
<item>ROI estimation of 'suit' atlas 3s</item>
<item>ROI estimation of 'ibsr' atlas 6s</item>
<item>ROI estimation of 'aal3' atlas 9s</item>
<item>ROI estimation of 'mori' atlas 12s</item>
<item>ROI estimation of 'anatomy3' atlas 16s</item>
<item>ROI estimation of 'julichbrain' atlas 22s</item>
<item>ROI estimation of 'Tian_Subcortex_S4_7T' atlas 3s</item>
<item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 9s</item>
<item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 18s</item>
<item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 40s</item>
<item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 53s</item>
<item>Write results 55s</item>
<item>245s</item>
<item>Quality check 10s</item>
<item>/var/lib/condor/execute/dir_1648529/ds/sub-12/report/catreport_sub-12_T1w.pdf</item>
<item>------------------------------------------------------------------------</item>
<item>CAT preprocessing takes 19 minute(s) and 27 second(s).</item>
<item>Image Quality Rating (IQR): 82.45% (B-)</item>
<item>GM volume (GMV): 50.81% (753.43 / 1482.84 ml)</item>
<item>Segmentations are saved in /var/lib/condor/execute/dir_1648529/ds/sub-12/mri</item>
<item>Reports are saved in /var/lib/condor/execute/dir_1648529/ds/sub-12/report</item>
<item>Labels are saved in /var/lib/condor/execute/dir_1648529/ds/sub-12/label</item>
<item>------------------------------------------------------------------------</item>
</catlog>
</S>
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