Re: [Freesurfer] long_mris_slopes command: temporal average calculation

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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