Hi Meena,
>From the recon-all log, it appears that you might actually be using an
>out-dated MNI distribution (1.14) instead of the one that ships with
>freesurfer (1.15). When you source freesurfer 6.0, the following mni path
>should be displayed:
MNI_DIR /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/mni
Are you seeing something different? If so, this might be because you have the
MNI_DIR, MNI_DATAPATH, or MNI_PERL5LIB env variables set to alternative mni
installs.
best
Andrew
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Meena M. Makary
<meena.maghari...@gmail.com>
Sent: Thursday, November 21, 2019 2:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all Error
External Email - Use Caution
Thank you, Doug! So here's what I've tried now.
I want to confirm first that this is the only subject that is failed so far. I
re-ran it in a different subject folder name and it failed too.
I ran it again without the -3T option and failed as well with the same error
(attached the log file "named with _no3T").
I am attaching also a log file of one other random subject who ran successfully
with the 3T option.
This is a part of patient population that was acquired at Bay 6, and this
subject (that failed) has a huge aliasing effect. I corrected it by centering
the image. we have few subjects who has this effect but were not as big as this
subject.
Thank you so much for taking the time to look into this.
Best,
Meena
On Thu, Nov 21, 2019 at 1:56 PM Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
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>
> <mailto: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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--
—
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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