Message: 3 Date: Tue, 2 Feb 2016 14:17:02 -0500 From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: E8AA9D81-BB67-446A-BDD8-2000A5AAC28B@nmr.mgh.harvard.edu Content-Type: text/plain; charset="us-ascii" Hi Will There was no attachment Bruce > On Feb 2, 2016, at 3:27 AM, will brown willbrown1987@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. >
- Ignored: > Thanks, > > Will > > > On Tue, Jan 26, 2016 at 6:00 AM, < freesurfer-request@nmr.mgh.harvard.edu> wrote: > > > Message: 1 > Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) > From: Bruce Fischl fischl@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.2.20.1601241858240.29174@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
- Done.
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---------- Forwarded message ---------- From: will brown willbrown1987@gmail.com To: freesurfer-request@nmr.mgh.harvard.edu Cc: Date: Thu, 4 Feb 2016 17:07:23 +1300 Subject: Re: mritotal failed - help with manual registration (Bruce Fischl) (Bruce Fischl) Sorry - attached now
Message: 3 Date: Tue, 2 Feb 2016 14:17:02 -0500 From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: E8AA9D81-BB67-446A-BDD8-2000A5AAC28B@nmr.mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
Hi Will
There was no attachment Bruce
On Feb 2, 2016, at 3:27 AM, will brown willbrown1987@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-request@nmr.mgh.harvard.edu
wrote:
Message: 1 Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) From: Bruce Fischl fischl@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.2.20.1601241858240.29174@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
