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McIntosh-Lab / tvb-ukbb

TVB-UKBB Pipeline: TheVirtualBrain implementation of the UK Biobank pipeline
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file T1_brain_pve_2 unable to be opened by fslmaths #12

Closed noahfl closed 4 years ago

noahfl commented 4 years ago

Unsure if this is due to the file being corrupt/improperly written or it not existing at all. WIll investigate

logfile bb_postprocess_struct_sub-002S0413.eXXXXXXX

+ direc=/liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413/                                                                                                                                                                    
+ linkDir=/liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//fMRI/symlink                                                                                                                                                     
+ mkdir /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//fMRI/symlink                                                                                                                                                       
+ ln -s ../../T1/T1.nii.gz /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//fMRI/symlink/T1.nii.gz                                                                                                                          
+ ln -s ../../T1/T1_brain.nii.gz /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//fMRI/symlink/T1_brain.nii.gz                                                                                                              
+ ln -s ../../T1/transforms/T1_to_MNI_warp.nii.gz /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//fMRI/symlink/T1_brain2MNI152_T1_2mm_brain_warp.nii.gz                                                                    
+ ln -s ../../T1/transforms/T1_to_MNI_linear.mat /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//fMRI/symlink/T1_brain2MNI152_T1_2mm_brain.mat                                                                             
+ /opt/fsl/bin/fslmaths /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//T1/T1_fast/T1_brain_pve_2.nii.gz -thr 0.5 -bin /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//fMRI/symlink/T1_brain_wmseg.nii.gz            
Cannot open volume /liberatrix/mcintosh_lab/nfrazier-logue/sub-002S0413//T1/T1_fast/T1_brain_pve_2 for reading!
shen4brains commented 4 years ago

I think this is a simple typo in the directory structure; will fix in my next commit