subject:"\[Freesurfer\] mritotal failed \- help with manual registration \(Bruce Fischl\)"

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

2016-02-04 Thread Bruce Fischl


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 <fis...@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-bdd8-2000a5aac...@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 <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.
    >

- Ignored:
    > Thanks,
    >
    > Will
    >
    >
    > On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-requ...@nmr.mgh.harvard.edu>
    wrote:
    >
    > 
    > 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

- Done.



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-- Forwarded message --
From: will brown <willbrown1...@gmail.com>
To: freesurfer-requ...@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 <fis...@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-bdd8-2000a5aac...@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 <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:
>
>
>
> Message: 1
> Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST)
> From:

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

2016-02-02 Thread Bruce Fischl

Hi Will

There was no attachment
Bruce

> On Feb 2, 2016, at 3:27 AM, will brown  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,  
> 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 segmentationwith FLAIR
>   (Luigi Antelmi)
>7. Re: hippocampal subfields - multispectral segmentationwith
>   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 
> Subject: Re: [Freesurfer] mritotal failed - help with manual
> registration
> To: Freesurfer support list 
> Message-ID:
> 
> 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

2016-02-02 Thread will brown

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,  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 segmentationwith FLAIR
  (Luigi Antelmi)
   7. Re: hippocampal subfields - multispectral segmentationwith
  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 
Subject: Re: [Freesurfer] mritotal failed - help with manual
registration
To: Freesurfer support list 
Message-ID:

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

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

2016-01-28 Thread Bruce Fischl

Hi Will

it looks like there is incomplete myelination, which is probably part of 
your problem. You could try manually adjusting the transform in 
tkregister2

cheers
Bruce
On Thu, 28 Jan 2016, will brown 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, 
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 
  Subject: Re: [Freesurfer] mritotal failed - help with manual
          registration
  To: Freesurfer support list 
  Message-ID:

  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
  >
  >

  --

  Message: 2
  Date: Sun, 24 Jan

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)

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