Hi Andreas: Very kind of you to share your code. I am sure many of us will benefit from this.
thanks, Alan Francis On Mon, Jul 21, 2014 at 9:12 AM, Andreas Berger < n0642...@students.meduniwien.ac.at> wrote: > Hello FreeSurfers, > > during the course of my diploma thesis i wrote a few R functions around > FreeSurfer, mainly for group analysis of FreeSurfer surface data in R. I > thought i'd just contribute the code here, on the off chance that > someone may find it useful, and despite the code quality (i wrote this > as part of me learning R, so it may actually set your house on fire and > so on). It could be of use for someone already working in R and looking > to bring FreeSurfer data into it, or someone looking for an alternative > to QDEC and the plots created by QDEC. Hardware requirement is not > entirely modest unfortunately; it eats up about 8G of memory and takes > about 15 minutes around here. > > > Here's an example of how it is used: > > > ############################ BEGIN R CODE ############################## > # Presupposing that you have a dataframe 'data' containing your group > # description and that all subjects have been processed in ~/subjects > > ### Group analysis with lm ### > # Run the model. This takes some time and memory. > lm <- freesurfer.group.analysis.lm(data = data, formula = thickness ~ > Age + Gender + Diagnosis, hemi = "lh", fwhm = 10, template = > "fsaverage", freesurfer_subjects_dir = "~/subjects") > > # Extract t values from the model, do FDR correction > t <- freesurfer.group.analysis.lm.stats(lm, type.of.value = "t", > correction="fdr") > > # Write the t values to mgh files and open them in FreeSurfer's freeview > freesurfer.group.analysis.lm.stats.to.mgh(t, hemi = "lh", template = > "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.freeview = > TRUE) > > # Write the t values to .dset ASCII files and open them in AFNI's SUMA > freesurfer.group.analysis.lm.stats.to.suma(t, hemi = "lh", template = > "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.suma = TRUE) > > # Make nice plots for vertex #1000 > freesurfer.group.analysis.lm.plot(lm, vertex = 1000, interactive = TRUE) > > > ### Group analysis with QDEC ### > # Call QDEC > freesurfer.group.analysis.QDEC(data = data, freesurfer_subjects_dir = > "~/subjects") > > > ### Extract stats ### > # Get segmentation stats > segstats <- freesurfer.get.segstats(subjects = data$ID, > freesurfer_subjects_dir = "~/subjects") > ############################## END R CODE ############################## > > > i uploaded the R package here, i called it freesurfR: > https://www.nitrc.org/projects/freesurf_r/ > > thanks also goes to Heath Pardoe, whose code for reading and writing MGH > files (also posted on this list) i was allowed to include. > > > regards, > Andreas > _______________________________________________ > 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. > >
_______________________________________________ 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.
