Hi Bruce, I attached the recon-all.log! Thanks in advance for taking a look! Darko
Message: 3 Date: Sat, 31 Mar 2018 06:47:12 -0400 From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 23B23889-C042-4A04-9316-4C8ED5468428@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8
Can you send us the recon-all.log?
On Mar 30, 2018, at 11:32 AM, Darko Komneni? komnenicd@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=s... 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