Can you send us the recon-all.log? > On Mar 30, 2018, at 11:32 AM, Darko Komnenić <komnen...@gmail.com> wrote: > > Dear experts, > while running recon-all on FreeSurfer 5.1.0 I encountered the following error: > mri_watershed Error: indices out of bounds > > I searched the email archive and found this thread: > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22&o=newest&f=1 > My problem seems identical to the one described by initial poster. > The suggestion was to try the following command: > set mdir=$SUBJECTS_DIR/$subject/mri > mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz > $mir/nu.mgz > > When I tried it, the message I got was: > mri_add_xform_to_header: could not open source file /nu.mgz > No such file or directory > And indeed such file does not exist in the mri subfolder of my > current subject's folder. > > Any further suggestions on how to fix this? Like the person asking > originally, this is the only participant where it happened, for > others, recon-all finished without error and all the images were > acquired in the same scanner. > Thanks in advance! > Best, > Darko > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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