I don't generally discourage it, but I don't think many people use it, and so it might not be maintained that well. But the error you are seeing appears to be that the mritotal program cannot be found (not a computational problem or problem with your data). But it is strange that you could run it with your other subjects; I would have thought that it would have failed for all of them. Can you re-run one of your subjects that failed (put it in a different subject name folder). You don't need to run the whole thing, just until it fails or subject/mri/transforms/talairach.xfm has been created.
Also, I looked at your data and noticed that the subject's head is at a rather extreme angle relative to the bore. Is this typical for your subject set? It could be causing a problem with the program doing the registration. On 11/21/19 1:11 PM, Meena M. Makary wrote: > > External Email - Use Caution > > Thank you, Douglas, for your fast reply. I have used -3T option for > all my dataset (>80 subject so far) and it worked well for all except > for this subject. Do you generally discourage using this option? I > thought it does some normalization/denoising for 3T scanners. I > haven’t had a chance to look deeper into it. Please let me know what > you think about it? > > Thank you! > Meena > > On Wed, Nov 20, 2019 at 5:51 PM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > This is something that is being triggered by use -3T. Is there a > reason > you are using that option? > > On 11/19/19 5:15 PM, Meena M. Makary wrote: > > > > External Email - Use Caution > > > > Hi, > > > > I have been getting this error with one of my subjects > Recon-all. I am > > attaching the recon-all log file. any help would be appreciated! > > > > Meena > > > > -- > > — > > *Meena M. Makary, Ph.D.* > > Assistant Professor|Cairo University <http://bmes.cufe.edu.eg/> > > Postdoctoral Fellow|Radiology, Harvard Medical School > > > <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> > > Postdoctoral Fellow| Athinoula A. Martinos Center, MGH > > <https://www.nmr.mgh.harvard.edu/user/4550386> > > Career Development and Mentoring Manager | OHBM Student and Postdoc > > SIG > <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > — > *Meena M. Makary, Ph.D.* > Assistant Professor|Cairo University <http://bmes.cufe.edu.eg/> > Postdoctoral Fellow|Radiology, Harvard Medical School > <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> > Postdoctoral Fellow| Athinoula A. Martinos Center, MGH > <https://www.nmr.mgh.harvard.edu/user/4550386> > Career Development and Mentoring Manager | OHBM Student and Postdoc > SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
