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 <skoga...@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
><mreu...@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
>> > <mreu...@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
>> > > <mreu...@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 <skoga...@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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>> > >
>> > >
>> >
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >
>> > > --
>> > > Sent from my phone, please excuse brevity.
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>for
>> > the person
>> > > to whom it is
>> > > addressed. If you believe this e-mail was sent to
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>> > > and the e-mail
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>> > > Compliance HelpLine at
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>> > >
>> > >
>> > > --
>> >
>> >
>> >
>> >
>> >
>> >
>>
>>
>>
>
>
>--
>Shannon Kogachi
>Clinical Research Coordinator
>
>Neuroscience and MRI Research Program
>Department of Medicine
>JABSOM, University of Hawaii
>1356 Lusitana Street, 7th Floor
>Honolulu, HI 96813
>(808) 691 - 8763
--
Sent from my phone, please excuse brevity.
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