Hi Bruce,
I've attached a shot of the misalignment as seen in freeview.
Yes the original images were DICOM created in Siemens machine T1, 0.8 slice
thickness, can provide all DICOM tags if needed.
Thanks,
Will
On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-requ...@nmr.mgh.harvard.edu
> wrote:
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2. recon -all errors (Jasmin Alves)
3. Re: Processing .mnc files (Ankita Chatterjee)
4. Re: Processing .mnc files (Bruce Fischl)
5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg)
6. hippocampal subfields - multispectral segmentation with FLAIR
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7. Re: hippocampal subfields - multispectral segmentation with
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8. Re: recon -all errors (Bruce Fischl)
9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl)
10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg)
11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl)
12. FDR map: hide very little cluster (std...@virgilio.it)
13. [All] position available immediately (Bruce Fischl)
14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o
thresholded.mgh 1.3 = -log10(.05) (Douglas Greve)
15. Re: FDR map: hide very little cluster (Douglas Greve)
16. R: Re: FDR map: hide very little cluster (std...@virgilio.it)
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18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve)
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----------------------------------------------------------------------
Message: 1
Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mritotal failed - help with manual
registration
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1601241858240.29...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Will
can you take the same images with freeview and send them along? Also:
tell us a bit about your images. What format did they start in? Were they
dicoms?
Bruce
On Mon, 25 Jan 2016, will brown wrote:
> Hi all,
> After attempting recon-all I received the error "mritotal failed, see
> transforms/talairach.log" etc which I understand may have something to do
> with bad output from registration. I've checked orig.mgz which does look
out
> of line - the orientation is off so that it appears the subject has their
> head tilted off to one side (see Image1.jpg).
>
> I have tried to fix this manually with the help of this tutorial:
>
> http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview
>
> Hovever, the "movable" blurry image that I'm trying to line up with my
> subjects image does not match the coronal, sagittal or horizontal views,
> e.g. when I click "coronal" my subject is displayed correctly but the
> movable image is displayed horizontally (see Image2.jpg and Image3.jpg).
>
> Am I missing something obvious? (and am I even on the right track given
this
> error?)
>
> Thanks in advance for any help.
>
> Cheers,
> Will
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