Hi Abid,
What troubles did you have with Spherical Demons? In any case, though using
a different interpolation method, if the registration is the same,
mris_preproc gives results very similar as the pycnophylactic method we
described in the paper, as long as the data is smoothed. However, before
smoothing, you need to consider the different face sizes (in this case, the
"vertex sizes"), as we show in the Appendix A of the paper. Currently this
step would need to be done outside mris_preproc.
A suggestion for running is (there are other ways, though):
1) Run mris_preproc as:
mris_preproc --s ${subj1} --s ${subj2} --s ${subj3} [...] --target
fsaverage --hemi ${h} --meas area --out ${h}-area-mrispreproc.mgh
--nocleanup
2) The --nocleanup option will keep the files for each subject. These can
be converted to ASCII with mris_convert (-c), and then the outputs
subjected to the correction we discuss in the Appendix. This correction can
be done with the command "rpncalc" as you may have seen in the webpage with
the documentation for the pycnophylactic method.
3) Once that has been done, the data can be smoothed, and then converted
back to other formats so that you can run the statistical analysis via,
e.g., mris_glmfit.
Note the above won't be using SD registration.
Hope this helps!
All the best,
Anderson
On 27 February 2015 at 20:41, <aqure...@nmr.mgh.harvard.edu> wrote:
> Hi Freesurfer group,
>
> I wanted to use mris_preproc to calculate regional differences in surface
> area between two groups.
>
> Ideally I would like to use something that is vertex-wise and preserves
> regional area, but I've had trouble with spherical demons (using the
> Winkler methodology). So I am going to first try using mris_preproc (and
> compare the two methods). I found this old thread suggesting that I should
> use the --area flag.
> But I had some questions:
>
> 1) Which surfname should I use with the --area flag? area.mid vs area.pial
> vs any other file
> 2) Should I use --meas flag in addition and if so which one? (similar to
> how --meas thickness is used for calculating cortical thickness)
> 3) Which --surfreg file should I use? sphere.reg vs sphere. Or do I not
> need the --surfreg?
>
>
> Thanks,
> Abid
>
>
> ---------- Forwarded message ----------
> From: Anderson M. Winkler <wink...@fmrib.ox.ac.uk>
> Date: Tue, May 14, 2013 at 1:19 AM
> Subject: Re: [Freesurfer] Usage of --area option in estimating the
> vertex-wise maps of surface area
> To: free <freesurfer@nmr.mgh.harvard.edu>
>
>
> Hi Xi-Nian,
>
> As Doug said, they don't do the same thing. The method in the paper
> uses a different kind of interpolation to allows the preservation of
> the amount of area, whereas mris_preproc achieves the same globally
> using a Jacobian correction. The results aren't expected to be
> identical at the vertex level or for small regions.
>
> An implementation of the method we proposed in the paper is available
> for Octave and/or Matlab at http://brainder.org/download/areal
> It works fine, but beware that it's quite slow.
>
> All the best,
>
> Anderson
>
>
>
> 2013/5/13 Douglas Greve <gr...@nmr.mgh.harvard.edu>
> >
> >
> > Hi Xi-Nian, it does not do the same thing, but it does something
> similar. Anderson found that it gave similar results in a lot of cases,
> but he has found some differences. If he's still following the FS list,
> maybe he can comment.
> >
> > doug
> >
> >
> >
> >
> >
> > On 5/11/13 9:53 PM, Xinian Zuo wrote:
> >
> > Hello Doug,
> >
> > I am doing some association studies between functional measures and
> surface area. In using mris_preproc, there is an option --area. Does
> this do sth similar to that as Winkler et al. (2012)?
> >
> > Winkler et al., 2012. Measureing and comparing brain cortical
> surfacearea and other areal quantities.
> >
> > Thank you very much.
>
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