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.htmlÂ
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 <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Surface statistics for PET
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <503806f3.50...@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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-----Original Message-----
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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)
----------------------------------------------------------------------
Message: 1
Date: Fri, 24 Aug 2012 18:45:54 +0000
From: "Herting, Megan" <mhert...@chla.usc.edu>
Subject: [Freesurfer] Control points and errors
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<7c6afe602753b44c84dc09c4d69f17b6a41...@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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Message: 2
Date: Fri, 24 Aug 2012 18:16:30 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] 3rd level surface analysis of fMRI data
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5037fd3e.6080...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
Hi Susan, sorry for the delay. If you want to use a random fx model,
then dont include any of the ffx options, so just
/mri_glmfit --y xrun/lh.cope1.mgh --osgm --glmdir xrun/lh.osgm.ffx
--surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/
doug
On 08/22/2012 07:21 PM, Susan Alice McLaughlin wrote:
> Hi,
>
> I?m a Freesurfer novice, and am confused about how to run a 3rd level
> cross-subject analysis on the surface using as input cross-run .gfeats
> from 10 subjects generated from a 2nd level analysis of fMRI data in FSL.
>
> Following the directions posted at
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I
> have sampled the .gfeat copes and varcopes into standard surface
> space, using /mris_preproc/.
>
> I would then go on to perform a 3rd level surface based analysis as
> the instructions suggest, using:
>
> /mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh
> --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh
> --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label/
>
> However, I want to use a random effects rather than fixed effects
> analysis. How do I do this? I tried /--yrfxvar/ as opposed to
> /--yffxvar/ but it didn?t work. And if I?m going to display the map
> resulting from this analysi! s, do I need to correct for multiple
> comparisons?
>
> Many thanks in advance,
>
> Susan McLaughlin
> Doctoral Candidate
> SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex)
> Dept. of Speech and Hearing Sciences
> University of Washington
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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