Thanks Martin! I will look into why we are not getting a sphere.reg file. Everything else seems pretty straight forward, although it sounds like the processing will be a lot easier with FS 5.1. Do you know when we could expect that to be released?
Best, Jonathan On Tue, Mar 29, 2011 at 1:39 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>wrote: > Hi Jonathan, > > sorry, missed your mail completely. > > Anyway, in 5.1 there will be tools to do all this automatically for you > (also for more than 2 time points). Everything below is only for 2 time > points. > > Also about your questions: > Something is wrong with you data, you should have the ?h.shpere.reg in > the surf directories. Make sure your long runs finish without error. > Make sure each subject has its own base (template). > > You would usually divide by the time difference in any case if your time > points are differently spaced between subjects: > mris_calc -o new.mgh whatever.mgh div 1.2 > (for example if time delta is 1.2 years) > > average thickness is (for 2 time points): > mris_calc -o avg.mgh tp1.mgh add tp2.mgh > mris_calc -o avg.mgh avg.mgh div 2 > > and dividing by avg thickness > mris_calc -o spc.mgh diff.mgh div avg.mgh > > Note that spc (symmetrized percent change) is recommended over percent > change with respect to time 1. Time 1 can be outlier and you get more > power using the symmetrized version (with respect to the average). > > Also note that mris_calc cannot deal with different input types (mgh and > curv files),therefore use mri_convert to convert a curv file into mgh > format, e.g. mri_convert lh.thickness lh.thick1.mgh > > For more than 2 time points you could fit a GLM within each subject to > compute the average and slope per time unit. But it depends on what you > are trying to achieve, one could also compare rate of change in first > year vs. rate of change in second year for a 3 tp study (each a year > apart). Or more complex longitudinal models.... > > Best, Martin > > On Wed, 2011-03-09 at 14:44 -0500, Jonathan DuBois wrote: > > Hi Freesurfer users, > > > > > > I have been working from the list posting below for vertex comparison > > of longitudinal thickness data, although there are a couple issues I > > was hoping someone could help with. > > > > Using FS v5.0 with the fixed binaries > , I have put together the following steps for data comparison following > the third step of the longitudinal stream with their associated commands > and questions (highlighted in bold). I am sorry if it is a lot of > information, although I thought it might be useful for other users > working with longitudinal analysis. > > > > > > Thanks > > > > Jonathan > > > > > > ------------------------------ > > > > > > Martin Reuter mreuter at nmr.mgh.harvard.edu > > > > Tue Jun 29 16:23:20 EDT 2010 > > > > > > Hi Sandra, > > > > (and the list, I think this might be interesting for others) > > > > > > 1. the longitudinal ?h.thickness files are in registration (within > > subject) > > > > so in order to compute the difference or the rate you can simply use: > > > > mris_calc -o lh.outdiff sdir2/surf/lh.thickness > > sdir1/surf/lh.thickness > > > > and for the rate, you can divide by time 1 thickness or by the average > > > > thickness. If the time points are not equally spaced across subjects, > > > > you can also divide by difference in time. > > > > It is best to smooth the thickness files before you do all this (i.e. > > > > within time point smooth the ?h.thickness files with mri_surf2surf). > > > > > > 2. then map everything to your template (e.g. fsaverage) with > > mri_surf2surf > > > > > > 3. there you can stack the thick-differences or thick-rates with > > > > mri_concat > > > > > > 4. do the glm > > > > > > Best > > > > Gruesse, Martin > > > > > > ------------------------------ > > > > > > 1. Smooth surface data: > > > > > > mri_surf2surf --s subj1_tp1.long.template --sval > > subj1_tp1.long.template/surf/lh.thickness --tval > > subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh --fwhm-src 10 > > --hemi lh > > > > > > mri_surf2surf: could not read > > surface > /space/mdeh2/1/halgdev/emcbkp/1/halgdev/projects/nyuproj/subjects/subj1_tp1.long.template/surf/lh.sphere.reg > > > > No such file or directory > > > > > > --The longitudinal processing does not create a ?h.sphere.reg or > > a ?h.sphere for running mri_register. While, the registration is > > specific to the longitudinal analysis, could I simply copy over > > the ?h.sphere.reg from the original subject, since it is the same > > brain? If not, how should this be generated? > > > > > > > > 2. Compare time point differences within subjects using mris_calc and > > one of the three options: > > > > > > a. divide tp2 by tp1 - [mris_calc -o lh.NC024_thick_diff_fwhm10.mgh > > subj1_tp2.long.template/surf/lh.thickness.fwhm10.mgh div > > subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh] > > > > b. divide by average thickness > > > > c. divide by between scan time difference > > > > > > --Option (a) is straight forward, although option (c) would be ideal > > given that our subjects vary in time between scans. How would option > > (b) or © be set up with mris_calc? Would mris_calc work for more than > > two time points? > > > > > > > > 3. Register subjects' between scan difference map to fsaverage > > > > > > mri_surf2surf --s lh.NC024_thickness_diff_fwhm10.mgh --trgsubject > > fsaverage --tval lh.NC024_thickness_diff_fsaverage.fwhm10.mgh > > --fwhm-src 10 --hemi lh > > > > > > --I haven't gotten to this step yet, but I'm not sure that it will > > work given that there is only a .mgh file without an associated > > subject? Also, similar problem to question one (no sphere.reg). > > > > > > 4. Stack subjects' difference maps using mri_concat > > > > > > 5. Run GLM using mri_glmfit > > > > _______________________________________________ > > 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. >
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