I see,
Usually people look at thickness maps and volume on an ROI basis. Volume on the surface I think is simply area times thickness. Not sure how meaningful that is as area of a vertex depends on the triangle mesh.

Anyway, you look at smoothed maps on fsaverage. The average volume for each vertex should be somewhere in the middle of the individual values across time after they have been resampled to fsaverage. You can find the mapped files in the base directories. Can you double check that the average is in the middle of the time points?
Best Martin

Shannon Kogachi <skogachi@gmail.com> wrote:
Hi Martin,
  I am running FS version 5.1.
This is the command line I ran:

long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage

These are the outputs I get, which are located in the subjects' base template surf folders:

lh.long.volume-rate.fwhm10.mgh
lh.long.volume-pc1.fwhm10.mgh
lh.long.volume-avg.fwhm10.mgh
lh.long.volume-spc.fwhm10.mgh
I also get the files that end in fsaverage.mgh.

I'm a little confused about this volume issue. In a previous post you said that "long_mris_slopes works for surface maps (both thickness and volume should work)." Therefore I used the long_mris_slopes for the volumes for a VBM analysis. Please let me know if this would not work. Thank you!

-Shannon

On Fri, Sep 28, 2012 at 4:02 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Shannon,

that cannot be. It either indicates a serious bug (which we have not yet
encountered in our data) or a problem with your processing.

Can you send me:
- the version you use
- the command line you run
- the output you get

Also long_mris_slopes is designed for analyzing surface maps (analysis
on a vertex by vertex basis). This is usually thickness. So I don't
understand what 'volumes' you mean? For an ROI analysis based on stats
files you need to use long_stats_slopes.

Best, Martin

On Thu, 2012-09-27 at 11:37 -1000, Shannon Kogachi wrote:
> Hi Martin,
>  Each subject has 3-6 timepoints. They are all about one year apart.
> Here's an example of the discrepancy: one subject with  5 timepoints
> had volumes that ranged from 2.2-2.4. However, from the
> long_mris_slopes command, the temporal average volume was calculated
> to be 1.67. Thanks for your help!
>
> -Shannon K.
>
> On Thu, Sep 27, 2012 at 6:21 AM, Martin Reuter
> <mreuter@nmr.mgh.harvard.edu> wrote:
>         Hi Shannon,
>
>         long_mris_slopes works for surface maps (both thickness and
>         volume
>         should work). In both cases it should compute the temporal
>         average.
>
>         I have another scripts that works for stats files
>         (long_stats_slopes) in
>         the same way.
>
>         How many time points do you have, how far apart (equally
>         spaced?).
>
>         Best, Martin
>
>         On Wed, 2012-09-26 at 14:59 -1000, Shannon Kogachi wrote:
>         > Hi Martin,
>         >    When I used the long_mris_slopes  command for the
>         thickness, the
>         > average thickness calculated in FreeSurfer was pretty
>         similar to
>         > averaging the values in FreeSurfer. Does this command only
>         work
>         > thickness measures and not for volume or area? Thanks!
>         >
>         > -Shannon
>         >
>         > On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter
>         > <mreuter@nmr.mgh.harvard.edu> wrote:
>         >         Hi Shannon
>         >
>         >         You probably mean average thickness.
>         >         My scripts compute the temporal average from the
>         linear fit
>         >         (at mid time), which can be differed from simply
>         averaging
>         >         values.
>         >         Best Martin
>         >
>         >         Shannon Kogachi <skogachi@gmail.com> wrote:
>         >                 Hi,
>         >                  I had a question about how the temporal
>         average is
>         >                 calculated for subjects with multiple
>         timepoints. I
>         >                 used the long_mris_slopes command on a
>         longitudinal
>         >                 set of data. However, when I compared the
>         average
>         >                 volumes calculated through this command to
>         the average
>         >                 volumes calculated in excel after extracting
>         the same
>         >                 vertices at the individual timepoints, these
>         values
>         >                 did not match up. The average volumes
>         calculated
>         >                 through long_mris_slopes were smaller.
>         Please let me
>         >                 know if there is a way to explain this
>         discrepancy.
>         >                 Thank you!
>         >
>         >                 -Shannon K.
>         >
>         >
>         >
>
>         >
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