External Email - Use Caution
> On November 21, 2019 at 7:56 PM "Greve, Douglas N.,Ph.D."
> <dgr...@mgh.harvard.edu> wrote:
> [...]
> 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.
Just something I noticed: the relevant error message from the log seems to be:
Can't locate shellwords.pl in @INC
ERROR: mritotal failed, see transforms/talairach.log
When I googled the first part about shellwords.pl, I found a reference to this
message:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50592.html
In it, it says:
"When there is an alignment failure using the talairach method
freesurfer reverts to mni tools. The mni tools will error out
with mritotal on more modern linux platforms because mritotal references
shellwords.pl which no longer ships with perl (starting around 5.14)."
That could explain why it works for most subjects.
Tim
> 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>
> > >
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> >
> >
> >
> > --
> > —
> > *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>
> >
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>
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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