Bruce Fischl Sat, 06 Sep 2014 07:00:14 -0700
Hi Larswhich surface are you using? If it's the white surface you might try looking at white matter volume to see if it is decreasingcheers Bruce On Sat, 6 Sep 2014, Lars M. Rimol wrote:Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: intercept(random effect) + centered age + group + group x centered age + sex I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this.... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
NorwayOn Mon, Oct 27, 2014 at 9:59 AM, Lars M. Rimol <larilin@gmail.com> wrote:Hi Bruce (and Jorge),Yes, it's the wm surface. I have also done the analyses with the pial surface and the results are similar to wm surface (attached p-maps: lh_0-1000_wmarea_s30_log10p_inflated_lateral.tif vs.
lh_0-1000_wmarea_s30_log10p_inflated_lateral.tif).
To your second question: White matter volume increased over this time period (lme analysis; controls: logP = 8.49, patients: logP = 6.34).
Since the cortical analyses were done using lme, which can handle missing data, some of the subjects have only one time point. So I created a difference map for
those subjects for whom we have data on both time points, to see if area on the first time point is consistently larger than on the second time point. Almost all subjects
showed larger values on tp1 than tp2 and the maps of average area change (across subjects) confirm that (attached file: lh_diff_vo-v2_rawdata_lateral.tif shows timepoint1 - timepoint2).
In addition, I ran an lme analysis with the same subjects and found results very similar to those for the entire sample (attached file: lh_2tp_01000_pmap_lateral.tif ).
Would you agree that this apparent reduction in cortical area seems plausible? There is a reduction over time in raw data, and pial surface area show the same trend as wm surface,
and the lme analysis with only subjects that have data on both time points shows very similar results as the lme with all subjects.
On the other hand, I suppose we wouldn't expect increased wm volume together with reduced area?
As for the effect size maps, I have worked on finding a way to represent change in area over time that is intuitive for a reader not familiar with FreeSurfer:
I figured one solution could be to log transform the dependent variable (wm or pial area). This way the significance tests are done with log transformed data and for purposes of illustration
I do exp(beta)*100-100 on the beta for time, which ensures that if there is e.g. a 1% reduction, the figure shows -1, and 1 for a 1% increase. I find this is a good way of demonstrating the
effects (attached figure: lh_wmarea_logtransf_expBeta2_s30_inflated_lateral.tif ). What do you think?
I could of course also transform the dependent variable into percentages. That is, baseline == 100 and tp2 expressed in percent of baseline. However, I find this to be a less attractive solution because
we basically lose the baseline values, and this makes the model less useful for all other purposes. For instance, we can't investigate group differences at the various time points within the model.
Perhaps more importantly, it's unclear what assumptions we are making. The lme assumes a normal distribution and it's unclear to me what the distribution of such ratios are.
Thank you!
LMR
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Douglas N Greve Tue, 09 Sep 2014 08:24:37 -0700
This is tough to interpret, but basically, yes it would be
0-.004mm2/year. It is not quite right to say that it is at that vertex
because of smoothing, but in that area. It is also hard to say what the
total change would be for a cluster. One could sum the changes over the
cluster vertices, but that would probably over-estimate the change.
doug
Hi Lars
which surface are you using? If it's the white surface you might try looking at white matter volume to see if it is decreasing
cheers
Bruce
On Sat, 6 Sep 2014, Lars M. Rimol wrote:
Hi,
I have performed a longitudinal analysis using the lme module in FreeSurfer,
with this model:
intercept(random effect) + centered age + group + group x centered age + sex
I tested the effect of time with this contrast vector [ 0 1 0 0 0 ].
Dependent variable is area.
Here, mapping the second beta means mapping the effect size for (change
over) time. In the beta map, I find values from 0 to 0.004. I would
interpret that to mean that local area shrinks by at most 0.004 mm² per year
in the reference group. But I'm not 100% sure about the biological (or
geometrical) meaning of that.
Can I interpret this literally as the mean yearly shrinkage of the three
triangles surrounding a given vertex, the average of whose area comprises
the area score of the vertex, being 4/1000 mm? Of course, these maps are
smoothed with 30mm, so the real spatial resolution is nowhere near this....
Thank you!
--
yours,
Lars M. Rimol, PhD
St. Olavs Hospital
Trondheim,
Norway
_______________________________________________yours,
Lars M. Rimol, PhD
Norwegian University of Science and Technology (NTNU)
Trondheim,
Norway