Hi Will

I expect that means that the talairach.xfm is off by a ton (i.e. by a 90 deg rotation or more). You are probably better off starting with the identity matrix.

cheers Bruce

On Thu, 4 Feb 2016, will brown wrote:

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