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]> wrote: > I would delete ${StudyFolder}/${Subject}/T1w/${Subject} > > Peace, > > Matt. > > From: <[email protected]> on behalf of Darko Komnenić > <[email protected]> > Date: Monday, May 7, 2018 at 10:36 AM > To: "[email protected]" <[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] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
