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

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Today's Topics:

1. Control points and errors (Herting, Megan) 2. Re: 3rd level surface analysis of fMRI data (Douglas N Greve) 3. Re: In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab (Jeff Sadino) 4. Re: problem with tksurfer (Douglas N Greve) 5. Re: In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab (Douglas N Greve) 6. Re: Surface statistics for PET (Douglas N Greve) 7. Re: mri_segstats error (Douglas N Greve) 8. Re: qdec analyses without interaction effect (Douglas N Greve) 9. tracula trac-all error malloc_error_break (Cat Chong) 10. Re: creating labels, new atlas (Bruce Fischl) 11. Re: creating a gca file from .mgz files (Bruce Fischl) 12. Re: Control points and errors (Bruce Fischl)

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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 are <110 and not next to a gray matter voxel) and send it through again. This will 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 fix 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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