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- <filedata>
- <path>/var/lib/condor/execute/dir_27215/ds/sub-AL027</path>
- <file>sub-AL027_ses-4_acq-RARE_T1w</file>
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- <Fm>/var/lib/condor/execute/dir_27215/ds/sub-AL027/mri/msub-AL027_ses-4_acq-RARE_T1w.nii</Fm>
- <Fp0>/var/lib/condor/execute/dir_27215/ds/sub-AL027/mri/p0sub-AL027_ses-4_acq-RARE_T1w.nii</Fp0>
- <fnames>..15/ds/sub-AL027/sub-AL027_ses-4_acq-RARE_T1w</fnames>
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- <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>
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- <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_1980</bids_folder>
- <bids_yes>0</bids_yes>
- <nproc>64</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>
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- <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>
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- <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>
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- <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>
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- <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>
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- <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>
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- <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>
- </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>
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- <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>
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- <restypes>
- <optimal>[1 0.3]</optimal>
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- <LASmyostr>0</LASmyostr>
- <pbtmethod>pbt2x</pbtmethod>
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- <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>
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- <item>/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_6_Dartel.nii</item>
- </darteltpms>
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- <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>
- <inv_weighting>[true]</inv_weighting>
- <histth>[0.96 0.9999]</histth>
- <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>
- <AMAPframing>1</AMAPframing>
- </extopts>
- </parameter>
- <qualitymeasures>
- <software/>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>8.34874443817876</SurfaceDefectArea>
- <SurfaceDefectNumber>10</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.14781978726387</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.443451821804047</SurfacePositionRMSE>
- <res_vx_vol>[1.5 4.5 1.5]</res_vx_vol>
- <res_vx_voli>[1 1 1]</res_vx_voli>
- <res_RMS>2.87228132326901</res_RMS>
- <res_BB>0</res_BB>
- <tissue_mn>[9.13330004430737e+18 6.60365628111103e+19 NaN NaN]</tissue_mn>
- <tissue_mnr>[NaN NaN NaN NaN]</tissue_mnr>
- <tissue_std>[1.31815948805665e+19 1.20733015406477e+19 1.39084999993328e+19 7.79566687043157e+18]</tissue_std>
- <tissue_stdr>[NaN NaN NaN NaN]</tissue_stdr>
- <contrast>NaN</contrast>
- <contrastr>NaN</contrastr>
- <NCR>0</NCR>
- <ICR>NaN</ICR>
- </qualitymeasures>
- <qualityratings>
- <res_vx_vol>[3 9 3]</res_vx_vol>
- <res_RMS>5.74456264653803</res_RMS>
- <res_BB>0.5</res_BB>
- <tissue_mn>[8.62400054931641 8.62400054931641 NaN NaN]</tissue_mn>
- <tissue_std>[8.624 8.624 8.624 8.624]</tissue_std>
- <contrast>NaN</contrast>
- <contrastr>NaN</contrastr>
- <NCR>0.5</NCR>
- <ICR>NaN</ICR>
- <SurfaceEulerNumber>2.42857142857143</SurfaceEulerNumber>
- <SurfaceDefectArea>3.08718610954469</SurfaceDefectArea>
- <SurfaceDefectNumber>1.5</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>2.95639586448669</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>8.8690357208252</SurfacePositionRMSE>
- <IQR>5.26778717548681</IQR>
- </qualityratings>
- <ratings_help>
- <qualitymeasures>
- <res_vx_vol>voxel dimensions</res_vx_vol>
- <res_RMS>RMS error of voxel size</res_RMS>
- <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>
- <system>LINUX</system>
- <version_spm>7771</version_spm>
- <version_matlab>9.3</version_matlab>
- <version_cat>12.8.1</version_cat>
- <revision_cat>1980</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>20220711-212557</date>
- <cat_warnings>
- <item>
- <identifier>cat_run_job:failedBGD</identifier>
- <message>cat_run_job1639: Detection of background failed.</message>
- <level>1</level>
- </item>
- <item>
- <identifier>cat_run_job1639:nonT1contrast</identifier>
- <message>A non-T1 contrast was detected and the NEW EXPERIMENTAL </br>PIPELINE is used! If it is was a high-resolution T1 image, </br>the initial segmentation might have failed, probably due </br>to alignment problems (please check the image orientation).</message>
- <level>1</level>
- <data>[13679.08267 7494.90057 13200.67356 6942.15241 6032.85064 4171.10889]</data>
- </item>
- <item>
- <identifier>cat_main:skipLAS</identifier>
- <message>Skip LAS due to image contrast. Use global normalization.</message>
- <level>0</level>
- </item>
- </cat_warnings>
- </software>
- <subjectmeasures>
- <software/>
- <qualitymeasures>
- <software/>
- <SurfaceEulerNumber>30</SurfaceEulerNumber>
- <SurfaceDefectArea>8.34874443817876</SurfaceDefectArea>
- <SurfaceDefectNumber>10</SurfaceDefectNumber>
- <SurfaceIntensityRMSE>0.14781978726387</SurfaceIntensityRMSE>
- <SurfacePositionRMSE>0.443451821804047</SurfacePositionRMSE>
- </qualitymeasures>
- <EC_abs>30</EC_abs>
- <defect_size>8.34874443817876</defect_size>
- <vol_abs_CGW>[171.764858823529 2.26238039215686 42.9481607843137 0 0]</vol_abs_CGW>
- <vol_abs_WMH>0</vol_abs_WMH>
- <vol_rel_WMH>0</vol_rel_WMH>
- <surf_TSA>288.023408670872</surf_TSA>
- <vol_TIV>216.9754</vol_TIV>
- <vol_rel_CGW>[0.791632870931587 0.0104268981283448 0.197940230940068 0 0]</vol_rel_CGW>
- <dist_thickness>
- <item>[0.79271096879117 0.264908003459406]</item>
- </dist_thickness>
- <dist_thickness_kmeans>[0.864399194717407 0.149601293569197 1]</dist_thickness_kmeans>
- <dist_thickness_kmeans_inner3>[0.65986701571586 0.0582006173354271 0.205860939206407;0.870164645032547 0.0415656137310215 0.496583685699084;1.01354687950788 0.0567694550897649 0.297555375094509]</dist_thickness_kmeans_inner3>
- <dist_thickness_kmeans_outer2>[0.297857157004654 0.159818241486289 0.764875129474048;1.27664999768131 0.190361195646461 0.235124870525952]</dist_thickness_kmeans_outer2>
- </subjectmeasures>
- <subjectratings>
- <vol_TIV>8.52789210830757</vol_TIV>
- <vol_rel_CGW>[10.5 0.5 1.40481736602134 0.5 0.5]</vol_rel_CGW>
- <vol_rel_WMH>1</vol_rel_WMH>
- <surf_TSA>8.21608089806654</surf_TSA>
- <SQR>8.58653716684124</SQR>
- </subjectratings>
- <ppe>
- <affreg>
- <skullstrippedpara>[0 1 0 4976.64 0.508410927131158]</skullstrippedpara>
- <skullstripped>[false]</skullstripped>
- <highBGpara>[0.0768952671553883 0.0601637346697705 0.349109172191021]</highBGpara>
- <highBG>[false]</highBG>
- </affreg>
- <SPMvols0>[36.9670078431373 59.7258549019608 365.580376470588 1563.00918431373 498.460576470588 2452.43483137255]</SPMvols0>
- <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>[0.0405870266258717 0.446597337722778 0.712586998939514 0 0]</dtc>
- <ll>[0.244248969118898 0 0.244248969118898 0;0.150092861851772 0.0295128915824142 0.179605753434186 18880.6953125;0.320830932470644 0.133047912158027 0.453878844628672 28372.201171875]</ll>
- <rmsdtc>[0.0888135209679604 0.909595429897308 1.47825288772583]</rmsdtc>
- <rmsgdt>[0.0627276450395584 0.53359055519104 0.82277113199234]</rmsgdt>
- <rmsdt>1.47825288772583</rmsdt>
- <dt>0.712586998939514</dt>
- </reginitp>
- <SPMvols1>[31.7449568627451 72.0606941176471 248.935850980392 1662.11398039216 510.151231372549 2451.82762352941]</SPMvols1>
- <tths>
- <gintnorm>
- <T3th>[13679.08267 7494.90057 13200.67356]</T3th>
- <Tth>
- <T3th>[-5.56234645843506 905.497314453125 8910.298828125 13019.44140625 13856.2333984375 30231.732421875]</T3th>
- <T3thx>[0 0.1 1 2 3 4]</T3thx>
- </Tth>
- </gintnorm>
- <uintnorm1postlas>
- <Tthm>
- <CGW>[0.295134992437725 0.804812478957717 0.748172909051623]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 0.885404977313176 2.24451872715487 2.41443743687315 4 5 6]</T3thx>
- </Tthm>
- <Tthmi>
- <CGW>[0.295135179417032 0.804809151851025 0.74817652557756]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 0.885405538251097 2.24452957673268 2.41442745555307 4 5 6]</T3thx>
- </Tthmi>
- </uintnorm1postlas>
- <uintnorm2postamap>
- <Tthm>
- <CGW>[0.35005610260843 0.57572676092079 1.1020640711807]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 1.05016830782529 1.72718028276237 3.30619221354209 4 5 6]</T3thx>
- </Tthm>
- <Tthmi>
- <CGW>[0.350056071694081 0.575724858365108 1.10206640961574]</CGW>
- <T3th>[0 0.333333333333333 0.666666666666667 1 1.33333333333333 1.66666666666667 2]</T3th>
- <T3thx>[0 1.05016821508224 1.72717457509532 3.30619922884722 4 5 6]</T3thx>
- </Tthmi>
- </uintnorm2postamap>
- </tths>
- <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>[0.023354310542345 0.121318392455578 0.357216238975525 0.413206160068512 0.428379118442535 1.30626308917999]</dtc>
- <ll>[0.27338046412459 0 0.27338046412459 0;0.278255677655678 0.0239466778591779 0.302202355514856 36773.1171875;0.177276046413936 0.0630568344235842 0.24033288083752 136148.28125;0.223288671017146 0.233830958236883 0.457119629254029 252133.375;0.202578949903193 0.245756752639404 0.448335702542597 429915.3125;0.202578949903193 0.245756752639404 0.448335702542597 429915.3125]</ll>
- <rmsdtc>[0.0319452397525311 0.18034690618515 0.556326687335968 1.30943858623505 2.64007019996643 2.50033974647522]</rmsdtc>
- <rmsgdt>[0.0130960643291473 0.0773437097668648 0.243668109178543 0.508467197418213 1.7252995967865 0.969367623329163]</rmsgdt>
- <rmsdt>2.50033974647522</rmsdt>
- <dt>1.30626308917999</dt>
- </reg>
- </ppe>
- <catlog>
- <item>------------------------------------------------------------------------</item>
- <item>CAT12.8.1 r1980: 1/1: ./ds/sub-AL027/sub-AL027_ses-4_acq-RARE_T1w.n</item>
- <item>------------------------------------------------------------------------</item>
- <item>SANLM denoising (medium): 2s</item>
- <item>------------------------------------------------------------------------</item>
- <item>WARNING 01: cat_run_job:failedBGD</item>
- <item>cat_run_job1639: Detection of background failed.</item>
- <item>------------------------------------------------------------------------</item>
- <item>Internal resampling (1.50x4.50x1.50mm > 1.00x1.00x1.00mm): 1s</item>
- <item>APP: Rough bias correction:</item>
- <item>Initialize 3s</item>
- <item>Estimate background 4s</item>
- <item>Initial correction 4s</item>
- <item>Refine background 2s</item>
- <item>Final correction 3s</item>
- <item>Final scaling 3s</item>
- <item>23s</item>
- <item>Correct center-of-mass 12s</item>
- <item>Affine registration 60s</item>
- <item>SPM preprocessing 1 (estimate 1 - TPM registration): 5s</item>
- <item>Use initial fine affine registration. 36s</item>
- <item>SPM preprocessing 1 (estimate 2): 27s</item>
- <item>----------------------------------------------------------------------------</item>
- <item>WARNING 02: cat_run_job1639:nonT1contrast</item>
- <item>A non-T1 contrast was detected and the NEW EXPERIMENTAL</item>
- <item>PIPELINE is used! If it is was a high-resolution T1 image,</item>
- <item>the initial segmentation might have failed, probably due</item>
- <item>to alignment problems (please check the image orientation).</item>
- <item>----------------------------------------------------------------------------</item>
- <item>SPM preprocessing 2 (write):</item>
- <item>Write Segmentation 8s</item>
- <item>Update segmentation 9s</item>
- <item>Update skull-stripping 6s</item>
- <item>Update probability maps 1s</item>
- <item>Update registration 29s</item>
- <item>53s</item>
- <item>Global intensity correction: SANLM denoising after intensity normalization (medium): 1s</item>
- <item>------------------------------------------------------------------------</item>
- <item>NOTE 01: cat_main:skipLAS</item>
- <item>Skip LAS due to image contrast. Use global normalization.</item>
- <item>------------------------------------------------------------------------</item>
- <item>15s</item>
- <item>SANLM denoising after LAS (medium) 15s</item>
- <item>16s</item>
- <item>--- Update Ym and Ymi ---</item>
- <item>ROI segmentation (partitioning):</item>
- <item>Atlas -> subject space 3s</item>
- <item>Major structures 1s</item>
- <item>Ventricle detection 4s</item>
- <item>Blood vessel detection 0s</item>
- <item>Manual stroke lesion detection 0s</item>
- <item>Closing of deep structures 0s</item>
- <item>Side alignment 1s</item>
- <item>Final corrections 2s</item>
- <item>10s</item>
- <item>Amap using initial SPM12 segmentations (MRF filter strength 0.07): 18s</item>
- <item>AMAP peaks: [1.10 0.04,0.40 0.05,0.61 0.07]</item>
- <item>--- Update Ym and Ymi ---</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 | 0.2734 0.0000 0.2734 | 32.0000</item>
- <item>2 | 2.50 | 0.2570 0.0054 0.2624 | 29.4886</item>
- <item>3 | 2.50 | 0.2514 0.0090 0.2604 | 26.9772</item>
- <item>4 | 2.50 | 0.2483 0.0108 0.2591 | 24.6107</item>
- <item>5 | 2.50 | 0.2459 0.0121 0.2580 | 22.6548</item>
- <item>6 | 2.50 | 0.2436 0.0131 0.2567 | 20.6989</item>
- <item>7 | 2.50 | 0.2408 0.0141 0.2550 | 18.9688</item>
- <item>8 | 2.50 | 0.2384 0.0152 0.2536 | 17.4455</item>
- <item>9 | 2.50 | 0.2358 0.0162 0.2520 | 15.9223</item>
- <item>10 | 2.50 | 0.2330 0.0175 0.2504 | 14.6627</item>
- <item>11 | 2.50 | 0.2301 0.0186 0.2487 | 13.4764</item>
- <item>12 | 2.50 | 0.2271 0.0197 0.2468 | 12.3015</item>
- <item>13 | 2.50 | 0.2238 0.0212 0.2450 | 11.3776</item>
- <item>14 | 2.50 | 0.2205 0.0224 0.2430 | 10.4537</item>
- <item>15 | 2.25 | 0.2783 0.0239 0.3022 | 9.5920</item>
- <item>16 | 2.25 | 0.2601 0.0351 0.2952 | 8.8725</item>
- <item>17 | 2.25 | 0.2508 0.0400 0.2908 | 8.1530</item>
- <item>18 | 2.25 | 0.2434 0.0432 0.2867 | 7.5234</item>
- <item>19 | 2.25 | 0.2368 0.0459 0.2826 | 6.9630</item>
- <item>20 | 2.25 | 0.2304 0.0478 0.2782 | 6.4027</item>
- <item>21 | 2.25 | 0.2239 0.0502 0.2741 | 5.9447</item>
- <item>22 | 2.25 | 0.2176 0.0521 0.2697 | 5.5083</item>
- <item>23 | 2.25 | 0.2114 0.0537 0.2650 | 5.0803</item>
- <item>24 | 2.25 | 0.2035 0.0560 0.2595 | 4.7404</item>
- <item>25 | 2.25 | 0.1975 0.0573 0.2548 | 4.4005</item>
- <item>26 | 2.25 | 0.1913 0.0587 0.2500 | 4.0868</item>
- <item>27 | 2.25 | 0.1850 0.0605 0.2456 | 3.8221</item>
- <item>28 | 2.25 | 0.1790 0.0617 0.2407 | 3.5574</item>
- <item>29 | 2.00 | 0.1773 0.0631 0.2403 | 3.3283</item>
- <item>30 | 2.00 | 0.1699 0.0643 0.2342 | 3.1221</item>
- <item>31 | 2.00 | 0.1645 0.0647 0.2292 | 2.9160</item>
- <item>32 | 2.00 | 0.1576 0.0660 0.2237 | 2.7495</item>
- <item>33 | 2.00 | 0.1524 0.0668 0.2192 | 2.5890</item>
- <item>34 | 2.00 | 0.1471 0.0675 0.2145 | 2.4330</item>
- <item>35 | 2.00 | 0.1417 0.0688 0.2105 | 2.3080</item>
- <item>36 | 2.00 | 0.1367 0.0696 0.2063 | 2.1830</item>
- <item>37 | 2.00 | 0.1317 0.0704 0.2021 | 2.0688</item>
- <item>38 | 2.00 | 0.1269 0.0715 0.1984 | 1.9714</item>
- <item>39 | 2.00 | 0.1223 0.0721 0.1944 | 1.8740</item>
- <item>40 | 2.00 | 0.1165 0.0730 0.1895 | 1.7907</item>
- <item>41 | 2.00 | 0.1124 0.0735 0.1859 | 1.7148</item>
- <item>42 | 2.00 | 0.1085 0.0738 0.1822 | 1.6390</item>
- <item>43 | 1.75 | 0.1046 0.0747 0.1793 | 1.5785</item>
- <item>44 | 1.75 | 0.1002 0.0760 0.1762 | 1.5194</item>
- <item>45 | 1.75 | 0.0968 0.0764 0.1732 | 1.4626</item>
- <item>46 | 1.75 | 0.0937 0.0769 0.1706 | 1.4166</item>
- <item>47 | 1.75 | 0.0909 0.0770 0.1679 | 1.3706</item>
- <item>48 | 1.75 | 0.0882 0.0772 0.1654 | 1.3290</item>
- <item>49 | 1.75 | 0.0845 0.0775 0.1620 | 1.2932</item>
- <item>50 | 1.75 | 0.0823 0.0774 0.1597 | 1.2574</item>
- <item>51 | 1.75 | 0.0802 0.0776 0.1577 | 1.2271</item>
- <item>52 | 1.75 | 0.0781 0.0777 0.1558 | 1.1992</item>
- <item>53 | 1.75 | 0.0762 0.0777 0.1539 | 1.1713</item>
- <item>54 | 1.75 | 0.0744 0.0779 0.1524 | 1.1493</item>
- <item>57 | 1.50 | 0.0759 0.0772 0.1531 | 1.0900</item>
- <item>Problem with Shooting (dets: 0.00380401 .. 3.17158)</item>
- <item>58 | 1.50 | 0.0701 0.0809 0.1510 | 1.0730</item>
- <item>59 | 1.50 | 0.0675 0.0819 0.1494 | 1.0579</item>
- <item>Shooting registration with 2.50:-0.25:1.50 mm takes: 370s</item>
- <item>Prepare output 7s</item>
- <item>377s</item>
- <item>Jacobian determinant (RMS): 0.032 0.180 0.556 1.309 2.640 | 2.500340</item>
- <item>Template Matching: 0.273 0.278 0.177 0.223 0.203 | 0.202579</item>
- <item>Write result maps: 18s</item>
- <item>Surface and thickness estimation:</item>
- <item>lh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 4s</item>
- <item>CSF distance: 2s</item>
- <item>PBT2x thickness: 5s</item>
- <item>13s</item>
- <item>Create initial surface 20s</item>
- <item>Topology correction: 20s</item>
- <item>Surface refinement: 44s</item>
- <item>Reduction of surface collisions with optimization: 21s</item>
- <item>Spherical mapping with areal smoothing 36s</item>
- <item>Spherical registration 336s</item>
- <item>rh:</item>
- <item>Thickness estimation (0.50 mm ):</item>
- <item>WM distance: 4s</item>
- <item>CSF distance: 2s</item>
- <item>PBT2x thickness: 6s</item>
- <item>13s</item>
- <item>Create initial surface 17s</item>
- <item>Topology correction: 93s</item>
- <item>Surface refinement: 117s</item>
- <item>Reduction of surface collisions with optimization: 47s</item>
- <item>Spherical mapping with areal smoothing 36s</item>
- <item>Spherical registration 370s</item>
- <item>Final surface processing results:</item>
- <item>Average thickness (FS): 0.7937 0.2502 mm</item>
- <item>Surface intensity / position RMSE: 0.1478 / 0.4435</item>
- <item>Euler number / defect number / defect size: 30.0 / 10.0 / 8.35%</item>
- <item>Display thickness: /var/lib/condor/execute/dir_27215/ds/sub-AL027/surf/lh.thickness.sub-AL027_ses-4_acq-RARE_T1w</item>
- <item>Display thickness: /var/lib/condor/execute/dir_27215/ds/sub-AL027/surf/rh.thickness.sub-AL027_ses-4_acq-RARE_T1w</item>
- <item>Show surfaces in orthview: /var/lib/condor/execute/dir_27215/ds/sub-AL027/sub-AL027_ses-4_acq-RARE_T1w.nii</item>
- <item>Surface ROI estimation: 1686s</item>
- <item>Surface and thickness estimation takes: 1655s</item>
- <item>ROI estimation in native space:</item>
- <item>ROI estimation of 'cobra' atlas 4s</item>
- <item>ROI estimation of 'neuromorphometrics' atlas 15s</item>
- <item>ROI estimation of 'lpba40' atlas 5s</item>
- <item>ROI estimation of 'hammers' atlas 11s</item>
- <item>ROI estimation of 'thalamus' atlas 1s</item>
- <item>ROI estimation of 'ibsr' atlas 4s</item>
- <item>ROI estimation of 'aal3' atlas 6s</item>
- <item>ROI estimation of 'mori' atlas 9s</item>
- <item>ROI estimation of 'anatomy3' atlas 13s</item>
- <item>ROI estimation of 'julichbrain' atlas 17s</item>
- <item>ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 7s</item>
- <item>ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 12s</item>
- <item>ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 28s</item>
- <item>ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 42s</item>
- <item>Write results 43s</item>
- <item>174s</item>
- <item>Quality check: 1s</item>
- <item>Print 'Graphics' figure to:</item>
- <item>/var/lib/condor/execute/dir_27215/ds/sub-AL027/report/catreport_sub-AL027_ses-4_acq-RARE_T1w.pdf</item>
- <item>------------------------------------------------------------------------</item>
- <item>CAT preprocessing takes 35 minute(s) and 28 second(s).</item>
- <item>Image Quality Rating (IQR): 52.32% (E-)</item>
- <item>GM volume (GMV): 1.04% ( 2.26 / 216.98 ml)</item>
- <item>GM thickness (GMT): 0.79 0.26 mm</item>
- <item>Segmentations are saved in /var/lib/condor/execute/dir_27215/ds/sub-AL027/mri</item>
- <item>Reports are saved in /var/lib/condor/execute/dir_27215/ds/sub-AL027/report</item>
- <item>Labels are saved in /var/lib/condor/execute/dir_27215/ds/sub-AL027/label</item>
- <item>------------------------------------------------------------------------</item>
- </catlog>
- </S>
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