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ds005479_cat12.9/sub-21/report/cat_sub-21_T1w.xml
Felix Hoffstaedter 28ba30be16 [DATALAD RUNCMD] Compute sub-21 
=== Do not change lines below ===
{
 "chain": [],
 "cmd": "singularity exec -B {pwd} --cleanenv code/pipeline/cat12.9_r2665.simg sh -e -u -x -c '\n        mkdir -p {outputs[0]} || true         && cp {inputs[0]} {outputs[0]}         && /singularity -b code/cat_standalone_segment_enigma_subdir_rp.m {outputs[0]}/*.nii.gz         && /singularity -b code/pipeline/batches/cat_standalone_batch-surfext.m {outputs[0]}/surf/lh.central.*         && /singularity -b code/pipeline/batches/cat_standalone_batch-thick1.m {outputs[0]}/surf/lh.thickness.*         && /singularity -b code/pipeline/batches/cat_standalone_batch-thick2.m {outputs[0]}/surf/lh.thickness.*         && rm -f {outputs[0]}/*.nii*         && gzip {outputs[0]}/*/*.nii         '",
 "dsid": "3827f929-f218-4211-9e52-9e59f1dcc1a2",
 "exit": 0,
 "extra_inputs": [
  "code/pipeline/cat12.9_r2665.simg"
 ],
 "inputs": [
  "inputs/ds005479/sub-21/anat/sub-21_T1w.nii.gz"
 ],
 "outputs": [
  "sub-21"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^
2025-05-23 03:12:19 +02:00

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<?xml version="1.0" encoding="utf-8"?>
<S>
<error>
<item/>
<item>Surface file /var/lib/condor/execute/dir_3991661/ds/sub-21/surf/lh.central.sub-21_T1w.gii could not be found due to previous processing errors.</item>
<item>1809 - loadSurf</item>
<item>1072 - cat_surf_createCS2</item>
<item>854 - cat_main1639</item>
<item>1438 - cat_run_job1639</item>
<item>40 - cat_run_newcatch</item>
<item>1335 - run_job</item>
<item>810 - cat_run</item>
<item>29 - cfg_run_cm</item>
<item>1717 - local_runcj</item>
<item>972 - cfg_util</item>
<item>479 - fill_run_job</item>
<item>257 - spm_jobman</item>
<item>115 - spm_standalone</item>
</error>
<filedata>
<path>/var/lib/condor/execute/dir_3991661/ds/sub-21</path>
<file>sub-21_T1w</file>
<fname>/var/lib/condor/execute/dir_3991661/ds/sub-21/sub-21_T1w.nii.gz</fname>
<F>/var/lib/condor/execute/dir_3991661/ds/sub-21/sub-21_T1w.nii</F>
<Fm>/var/lib/condor/execute/dir_3991661/ds/sub-21/mri/msub-21_T1w.nii</Fm>
<Fp0>/var/lib/condor/execute/dir_3991661/ds/sub-21/mri/p0sub-21_T1w.nii</Fp0>
<fnames>..ute/dir_3991661/ds/sub-21/sub-21_T1w</fnames>
</filedata>
<hardware>
<numcores>1</numcores>
</hardware>
<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>
<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>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>
<send_info>1</send_info>
<gifti_dat>1</gifti_dat>
<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>pbt2x</pbtmethod>
</extopts>
<caterr>
<item>
<line>1809</line>
<name>loadSurf</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_surf_createCS2.m</file>
</item>
<item>
<line>1072</line>
<name>cat_surf_createCS2</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_surf_createCS2.m</file>
</item>
<item>
<line>854</line>
<name>cat_main1639</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_main1639.m</file>
</item>
<item>
<line>1438</line>
<name>cat_run_job1639</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_run_job1639.m</file>
</item>
<item>
<line>40</line>
<name>cat_run_newcatch</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_run_newcatch.m</file>
</item>
<item>
<line>1335</line>
<name>run_job</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_run.m</file>
</item>
<item>
<line>810</line>
<name>cat_run</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/toolbox/cat12/cat_run.m</file>
</item>
<item>
<line>29</line>
<name>cfg_run_cm</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/matlabbatch/private/cfg_run_cm.m</file>
</item>
<item>
<line>1717</line>
<name>local_runcj</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/matlabbatch/cfg_util.m</file>
</item>
<item>
<line>972</line>
<name>cfg_util</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/matlabbatch/cfg_util.m</file>
</item>
<item>
<line>479</line>
<name>fill_run_job</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/spm_jobman.m</file>
</item>
<item>
<line>257</line>
<name>spm_jobman</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/spm_jobman.m</file>
</item>
<item>
<line>115</line>
<name>spm_standalone</name>
<file>/code/SPM/MCR_Linux/spm25_mcr/home/ubuntu/Desktop/spm12/spm_standalone.m</file>
</item>
</caterr>
</parameter>
<qualitymeasures>
<NCR>NaN</NCR>
<ICR>NaN</ICR>
<contrastr>NaN</contrastr>
<res_ECR>NaN</res_ECR>
<res_RMS>1.0000000006779</res_RMS>
</qualitymeasures>
<software>
<version_spm>25.01.02</version_spm>
<version_matlab>23.2</version_matlab>
<system>LINUX</system>
<version_cat>12.9</version_cat>
<version_segment>2665</version_segment>
<revision_cat>2665</revision_cat>
</software>
<subjectmeasures>
<vol_rel_CGW>[NaN NaN NaN]</vol_rel_CGW>
<SQR>NaN</SQR>
</subjectmeasures>
<help>
<qualitymeasures>
<res_RMS>RMS error of voxel size</res_RMS>
<res_ECR>normalized gradient slope of the white matter boundary</res_ECR>
<contrastr>contrast between tissue classes</contrastr>
<NCR>noise to contrast ratio</NCR>
<ICR>inhomogeneity to contrast ratio</ICR>
</qualitymeasures>
<subjectmeasures>
<vol_rel_CGW>relative tissue volume (CSF,GM,WM)</vol_rel_CGW>
</subjectmeasures>
</help>
<qualityratings>
<res_RMS>2.0000000013558</res_RMS>
<res_ECR>NaN</res_ECR>
<contrastr>NaN</contrastr>
<NCR>NaN</NCR>
<ICR>NaN</ICR>
<SIQR>NaN</SIQR>
<IQR>2.0000000013558</IQR>
</qualityratings>
<subjectratings>
<vol_rel_CGW>[NaN NaN NaN]</vol_rel_CGW>
<SQR>0</SQR>
</subjectratings>
</S>
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