Hi Greg,
Is this simply an image viewing problem or does the data actually need to be re-processed? (I'm working with ~500 subjects, so I figured I would check before taxing the servers I had access to).
Thanks much!
Best, Jamie.
On Thu, Oct 9, 2014 at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: Surface Viewer Issue. (Gregory Kirk)
- Re: Mismatched dimensions with T1 and Flair inputs {Disarmed} (Vilde)
- Re: v5.1 control point mri_ca_normalize bug (Marx, Gabe)
- Re: v5.1 control point mri_ca_normalize bug (Bruce Fischl)
- Re: rawfunc2surf-sess with a limited set of surface files (Douglas N Greve)
- functional correlation (Brian Donley)
- Re: rawfunc2surf-sess with a limited set of surface files (Reza Rajimehr)
- mri_thickness & mri_make_surfaces (Seung-Goo KIM)
- Re: WM & Pial Segmentation Errors (Varjabedian, Ani)
- "deployed" (compiled) MATLAB scripts path manipulation (slehar@nmr.mgh.harvard.edu)
- 8 spots remain in the FreeSurfer course (Allison Stevens)
- excluding labels (Adam, Ruth)
- FSGD Format Error (Retzepi, Kallirroi)
Message: 1 Date: Wed, 08 Oct 2014 14:47:27 -0500 From: Gregory Kirk gkirk@wisc.edu Subject: Re: [Freesurfer] Surface Viewer Issue. To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 76a0cbb215b316.54354e7f@wiscmail.wisc.edu Content-Type: text/plain; CHARSET=US-ASCII
i saw this problem on one redhat installation, not on any others, seems something with the X library orientation information and openGL
greg
On 10/08/14, Jamie Hanson wrote:
Hi Freesurfer List,
I had a (hopefully quick) question about surface viewers and data
orientation in tksurfer v. freeview.
I processed all my data in freesurfer v5.3.0 (on a linux cluster) and
noticed something odd when I viewed surfaces. For tksurfer, the surfaces were upside down when I opened them (see attached pic: tksurfer.png); for freeview, the data looked fine (see attached pic: freeview.png).
I believe the orientation of the images is correct (judging by the
freeview axes), but wondered if this was something others had run into? I uploaded an example subject to the Martinos Center FileDrop (link: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=9491zcnivqw).
Any thoughts are greatly appreciated! Thanks much!
Best, Jamie.
-- Jamie L. Hanson Postdoctoral Fellow, Carolina Consortium on Human Development Duke University 417 Chapel Drive Duke West Campus Sociology-Psychology Building, Room 07A Durham, NC 27710 Email: jamielarshanson@gmail.com Website: http://jamiehanson.org/
Message: 2 Date: Wed, 8 Oct 2014 22:01:06 +0200 From: Vilde vildeskard@hotmail.com Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs {Disarmed} To: freesurfer@nmr.mgh.harvard.edu Message-ID: DUB122-W3321C71B2BEC2FA5D6BE4CD2A30@phx.gbl Content-Type: text/plain; charset="iso-8859-1"
I will try that.
Have a good day!
Date: Wed, 8 Oct 2014 14:07:38 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
you would have to first run recon-all -all on the T1 On Wed, 8 Oct 2014, Vilde wrote:
Thank you Bruce!
If I understand you correctly, would the command be
Recon-all -s subj_name -FLAIRpial.nii ?
Or would I first have to do recon-all with only T1 as input and then do another command after it has finished running? And in that case, what
would
that command be?
Best, Vilde
Date: Wed, 8 Oct 2014 11:56:51 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mismatched dimensions with T1 and Flair inputs
Hi Vilde
no, you can't give recon-all a flair directly, it needs a T1 do do the recon on. You use the flair at the end to do a post-hoc deformation using -flairpial I believe
cheers Bruce
On Wed, 8 Oct 2014, Vilde wrote:
Dear mailing list, I am trying to do a recon-all with two nifti inputs: A T1 and a Flair,
for
pial surface refinement. This results in an error message saying the dimensions are mismatched. (The third dimension of the T1 and Flair are different by one slice. ) I do not, however, have a problem running recon-all with only one T1 input. I am using Freesurfer v 5.1 .
I read in the release notes that in version 5.2 you can use the flag
-FLAI
R
when you are using a flair image as input. I suppose this will not run
in
an
earlier version? Would it be correct to use the following command :
recon-all -s [subject] -i T1.nii -i flair.nii -all
Kind regards, Vilde
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Jamie Hanson