Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

2017-11-17 Thread Manoj Kumar 
Hello Dear Sir/Madam,

Please provide your expert suggestions to resolve the above-mentioned error.

Thank you very much,

Best regards
Manoj

On Sat, Nov 18, 2017 at 11:05 AM, Manoj Kumar  wrote:

> Hello Dear Sir/Madam,
>
> I am fairly new to the freesurfer and am getting an error "ERROR:
> mpr2mni305 failed, see transforms/talairach_avi.log"
>
> When I run the "recon-all -all -subjid Anj   commond.
>
> I looked for this error message on https://mail.nmr.mgh.
> harvard.edu/pipermail//freesurfer/2014-August/039761.html
> But could not resolve this issue by myself.
> I am here also attaching the complete error log and recon-all-error file
> for your find attention.
>
> Please kindly provide your expert suggestions to resolve this issue.
> Please let me know if you need any additional information for further
> diagnosis of the error.
>
> Thank you very much for all your help and support.
>
> Best
>
>
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Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

2011-05-17 Thread Nick Schmansky 
mri_convert -iks 1 --conform ga_2010.nii 001.mgz

will create an image where the z direction is 1mm.  but the orientation
will still be wrong, since it was missing from the header (or
incorrect).  orient_mri can be used to rotate it, but one cannot know
whether left or right is correct.

n.


On Mon, 2011-05-16 at 21:35 -0300, Pedro Paulo de Magalhães Oliveira
Junior wrote:
 The images are:  0.5 x 0.5 x 1.0
 
 
 Can mri_convert fix it or should I edit the Nifti header?
 
 2011/5/16 Nick Schmansky ni...@nmr.mgh.harvard.edu
 PPJ,
 
 Hi,
 
 mri_info /space/incoming/ga_2010.nii
 
 shows that the image is 0.5 x 0.5 x 0.5.  but when viewing in
 freeview
 or tkmedit, the brain seems 'squashed', as if there is a slice
 gap.  do
 you know the details of how this was acquired?
 
 N.
 
 
 
 On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães
 Oliveira
 
 Junior wrote:
  I'm having this error in the recon-all
 
 
  #
  #@# Talairach Mon May 16 16:38:01 EDT 2011
  /usr/local/freesurfer/subjects/GAGRICOLA/mri
 
 
   talairach_avi --i orig.mgz --xfm
 transforms/talairach.auto.xfm
 
 
  ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
 
 
  I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the
  talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the
 original
  nifti image as ga_2010.nii
 
 
  Any hints?
 
 
 
 
 
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 to whom it is
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 contains patient information, please contact the Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was
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 sender and properly
 dispose of the e-mail.
 
 

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[Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

2011-05-16 Thread Pedro Paulo de Magalhães Oliveira Junior 
I'm having this error in the recon-all

#
#@# Talairach Mon May 16 16:38:01 EDT 2011
/usr/local/freesurfer/subjects/GAGRICOLA/mri

 talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the
talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti
image as ga_2010.nii

Any hints?
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Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

2011-05-16 Thread Nick Schmansky 
PPJ,

Hi, 

mri_info /space/incoming/ga_2010.nii

shows that the image is 0.5 x 0.5 x 0.5.  but when viewing in freeview
or tkmedit, the brain seems 'squashed', as if there is a slice gap.  do
you know the details of how this was acquired?

N.



On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães Oliveira
Junior wrote:
 I'm having this error in the recon-all 
 
 
 #
 #@# Talairach Mon May 16 16:38:01 EDT 2011
 /usr/local/freesurfer/subjects/GAGRICOLA/mri
 
 
  talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm 
 
 
 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
 
 
 I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the
 talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original
 nifti image as ga_2010.nii
 
 
 Any hints?
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

2011-05-16 Thread Pedro Paulo de Magalhães Oliveira Junior 
The images are:  0.5 x 0.5 x 1.0

Can mri_convert fix it or should I edit the Nifti header?

2011/5/16 Nick Schmansky ni...@nmr.mgh.harvard.edu

 PPJ,

 Hi,

 mri_info /space/incoming/ga_2010.nii

 shows that the image is 0.5 x 0.5 x 0.5.  but when viewing in freeview
 or tkmedit, the brain seems 'squashed', as if there is a slice gap.  do
 you know the details of how this was acquired?

 N.



 On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães Oliveira
 Junior wrote:
  I'm having this error in the recon-all
 
 
  #
  #@# Talairach Mon May 16 16:38:01 EDT 2011
  /usr/local/freesurfer/subjects/GAGRICOLA/mri
 
 
   talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm
 
 
  ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
 
 
  I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the
  talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original
  nifti image as ga_2010.nii
 
 
  Any hints?
 
 
 
 
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  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.

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The information in this e-mail is intended only for the person to whom it is
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