Hi Will There was no attachment Bruce
> On Feb 2, 2016, at 3:27 AM, will brown <willbrown1...@gmail.com> wrote: > > 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: > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Re: mritotal failed - help with manual registration (Bruce Fischl) > 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 > (Luigi Antelmi) > 7. Re: hippocampal subfields - multispectral segmentation with > FLAIR (Eugenio Iglesias) > 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) > 17. R: Re: FDR map: hide very little cluster (std...@virgilio.it) > 18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve) > 19. R: R: Re: FDR map: hide very little cluster (std...@virgilio.it) > 20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N Greve) > 21. R: Re: R: Re: FDR map: hide very little cluster > (std...@virgilio.it) > > ---------------------------------------------------------------------- > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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