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. > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > > -- 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
_______________________________________________ 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.
