logs/ -q reconįreeSurfer Overview 🗂️ Page Index for this GitHub Wiki logs/ -q reconįor control point recon, or for white matter recon: $ echo "recon-all -autorecon2-wm -autorecon3 -subjid " | qsub -V -N -o. Now try reloading it on the queue with $ echo "recon-all -autorecon2-cp -autorecon3 -subjid " | qsub -V -N -o. In this case, you need to remove the file that makes the queue think this and reload the job onto the queue by doing the following: $ rm /path/to/subjects/directory/subjectfoldername/scripts/IsRunning.lh+rh Usually, this means that the queue believes that your job is still processing. If you notice that your job disappears from the iqstat queue after a few seconds (you may also see that the S column says E or that your job color is green), there's been an error. That will add it to the queue on ba3, and after ~24 hours it should be done, and you can review the brain.
$ echo "recon-all -autorecon-all -subjid " | qsub -V -N -o. $ export SUBJECTS_DIR=/path/to/subjects/directory This is similar to running CP and WM recon, except we tell FreeSurfer to recon from scratch with the -autorecon-all directive.
Now everything should be gone except mri/orig/001.mgz. There's usually a folder called transforms here, delete that too: Then go to the mri folder and delete all of the files. lovingly called Suaveciclos that they use to project original animations on almost any nearby public surface. $ rm -rf bem label scripts src stats surf tmp touch trash Usually they are bem, label, mri, scripts, src, stats, surf, tmp, touch, and trash. This will display all of the sub-folders. Now check to see what's in your subject's folder: If it doesn't, you won't be able to reprocess the brain from scratch and you shouldn't continue!! If 001.mgz is there, great! You can proceed. $ cd /path/to/subjects/directory/subjectfoldername Go to the subject's folder and before you do anything make sure mri/orig/001.mgz exists: Delete all of the brain's current files, EXCEPT mri/orig/001.mgz.To reprocess a brain from scratch, follow these steps: If you decide to do this, do it before you make any CP/WM edits so you don't waste your time. If the white matter surfaces contain many big errors, you may want to re-recon the brain from scratch - this will usually fix huge problems. It's possible for things to go wrong while editing brains - here we have some common issues.
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