I think that should be okay. Only issue would be if you had already run PostFreeSurfer which overwrites the T2w image with the registered one (which you would not want to rerun the registration on).
Peace, Matt. From: Darko Komnenić <[email protected]<mailto:[email protected]>> Date: Monday, May 7, 2018 at 10:58 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] A question about rerunning FS pipeline Hi Matt, the problem is that my manually corrected brainmask.mgz file is inside the {StudyFolder}/${Subject}/T1w/${Subject}/mri folder, so I don't really want to delete the whole thing. Also, in the FreeSurfer.sh file everything from #Make Spline Interpolated Downsample to 1mm until num_cores variable has been commented out, because (from what I understood) the script in between generates the brain mask, (which I manually corrected, so I don't want FS to generate it again). So the first script that gets executed now is # Call recon-all to run most of the "-autorecon2" stages, but turning off smooth2, inflate2, curvstats, and segstats stages So I was wondering if I can just rerun this "commented out" version of FS Pipeline without having to delete anything. Thanks! Darko On Mon, May 7, 2018 at 5:46 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: I would delete ${StudyFolder}/${Subject}/T1w/${Subject} Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Darko Komnenić <[email protected]<mailto:[email protected]>> Date: Monday, May 7, 2018 at 10:36 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] A question about rerunning FS pipeline Dear HCP experts, I am comparing cortical myelin content between patients and controls. I manually corrected some brainmasks and tried to rerun the FS pipeline, which failed at the HiResPial step, because I forgot that some lines of the script have been commented out. Can I just rerun everything (after returning the lines that were commented out) or should I first delete some files or folders? For example, should I delete the ribbon folder from Subject_name/T1w/Subject_name/mri subfolder? Basically, the FS pipeline ran fine until the HiResPial step. Thanks in advance for the replies! Best, Darko _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
