Fwd: Surface statistics for PET - Freesurfer

26 Aug 2012

      Hi Bruce,
I'm sorry I didn't ask the correct question - I was able to generate the .mgh 
file with mri_vol2surf without problem. 
The issue was that "qsurfer" gives me an error stating it couldn't find the .w file. According to usage it needs a file ending in -?h.w.  Is there a way to use a .mgh file with qsurfer, or is there a better way to view inflated functional data than with qsurfer?
Thank you again,
Daniel
Sent from my iPhone
On Aug 26, 2012, at 12:50 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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sure, use mgh as the output format of mri_vol2surf.
cheers
Bruce
On Sun, 26 Aug 2012, Daniel Tarquinio wrote:
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Thank you Doug, that worked perfectly.
Regarding the .w file, to view the functional data inflated I used this
tutorial:
http://poc.vl-e.nl/distribution/manual/fsl-3.2/freesurfer/index.html 
Is there a workaround to view inflated functional data mapped using
mri_vol2surf with a .mgh file?
Thank you again,
Daniel
Message: 6
Date: Fri, 24 Aug 2012 18:57:55 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface statistics for PET
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 503806F3.50807@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
You can use mri_segstats for this, something like
mri_segstats --annot subject lh aparc --i lh.pet.mgh --sum sum.dat
where lh.pet.mgh is the surface-sampled pet
BTW, unless you need a .w for something, use a .mgh file (the .w is becoming
obsolete).
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doug
On 08/23/2012 07:27 PM, Daniel Tarquinio wrote:
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I would like to calculate average PET intensities for specific labels >
(using the aparc.annot label files).
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I have coregistered and used mri_vol2surf to assign PET values to the > FS
generated surface, and viewed the results using qsurfer.
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The next step is to take the values from the .w files and calculate >
label-specific stats. I've tried mris_anatomical_stats but I don't > think this 
is the right command.
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Any advice?
Thank you in advance,
Daniel

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Today's Topics:

Control points and errors (Herting, Megan)
Re: 3rd level surface analysis of fMRI data (Douglas N Greve)
Re: In Qdec, what does the 'area' mean within 'Measure' menu
in 'Design' tab (Jeff Sadino)
Re: problem with tksurfer (Douglas N Greve)
Re: In Qdec, what does the 'area' mean within 'Measure' menu
in 'Design' tab (Douglas N Greve)
Re: Surface statistics for PET (Douglas N Greve)
Re: mri_segstats error (Douglas N Greve)
Re: qdec analyses without interaction effect (Douglas N Greve)
tracula trac-all error malloc_error_break (Cat Chong)
Re: creating labels, new atlas (Bruce Fischl)
Re: creating a gca file from .mgz files (Bruce Fischl)
Re: Control points and errors (Bruce Fischl)

Message: 1
Date: Fri, 24 Aug 2012 18:45:54 +0000
From: "Herting, Megan" mherting@chla.usc.edu
Subject: [Freesurfer] Control points and errors
To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Message-ID:
   7C6AFE602753B44C84DC09C4D69F17B6A41058@CHLAEXMBH01.LA.AD.CHLA.ORG
Content-Type: text/plain; charset="us-ascii"
Hi,
I have been using freesurfer on a large dataset and I am having some trouble
. Sometimes the temporal lobes are not fully covered, so I will go back to
add
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a few control points based on the recommendations of freesurfer (voxels that
a
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re <110 and not next to a gray matter voxel) and send it through again. This
wi
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ll often correct the previous error, but then ends up creating new errors in
a different region (frontal lobe, temporal lobe in the other hemisphere) etc. 
This has happened on a large fraction of my data (~25%). What is recommended to 
f
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ix this? Should I continue to  try to add cp to these new regions and send it
through again, and continue to do this until it looks good? Is there another
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method?
Thank you!
Megan

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