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:
sure, use mgh as the output format of mri_vol2surf.
cheers Bruce On Sun, 26 Aug 2012, Daniel Tarquinio wrote:
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).
doug On 08/23/2012 07:27 PM, Daniel Tarquinio wrote:
I would like to calculate average PET intensities for specific labels >
(using the aparc.annot label files).
I have coregistered and used mri_vol2surf to assign PET values to the > FS
generated surface, and viewed the results using qsurfer.
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.
Any advice?
Thank you in advance, Daniel
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-----Original Message----- From: freesurfer-request freesurfer-request@nmr.mgh.harvard.edu To: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sat, Aug 25, 2012 12:00 pm Subject: Freesurfer Digest, Vol 102, Issue 27 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-request@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner@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:
- 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
a few control points based on the recommendations of freesurfer (voxels that
a
re <110 and not next to a gray matter voxel) and send it through again. This
wi
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
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
method? Thank you! Megan
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