Hi Martin, I am a little confused about these mapped files in the base directories you are referring to. How would I check them?
-Shannon K. On Fri, Sep 28, 2012 at 4:08 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>wrote: > 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. >>> > > >>> > > >>> > > >>> > >>> > > >>> > ______________________________________________________ >>> > > >>> > > Freesurfer mailing list >>> > > Freesurfer@nmr.mgh.harvard.edu >>> > > >>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > > >>> > > -- >>> > > Sent from my phone, please excuse brevity. >>> > > 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. >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > -- >>> > >>> > >>> > >>> > >>> > >>> > >>> >>> >>> >> >> > -- > Sent from my phone, please excuse brevity. >
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