Sid, 1) when recon-all is finished on a subject, there are a number of stats found in the <subj>/stats directory. for the additional ones you want, you can use mris_anatomical_stats. see 'mris_anatomical_stats --help'. ex. mris_anatomical_stats -a aparc -t lgi subjid lh see also 'aparcstats2table' to group a collection of subjects.
2) you can use the -qcache option of recon-all (normally used to generate files used by the qdec app) to handle the resampling of data to a common surface (fsaverage). example: recon-all -s subj -qcache -measure lgi -fwhm 0 -hemi lh will create subj/surf/lh.lgi.fwhm0.fsaverage.mgh where fwhm is the amount of smoothing (0mm in this case means no smoothing). then, once you have this file for every subject, to get a mean, you can use: mri_concat --i subj1/surf/lh.lgi.fwhm0.fsaverage.mgh \ subj2/surf/lh.lgi.fwhm0.fsaverage.mgh \ subj3/surf/lh.lgi.fwhm0.fsaverage.mgh ... \ --mean \ --o mygroup.lh.lgi.fwhm0.mean.fsaverage.mgh 3) there is no way to change the colors in the tkmedit/tksurfer colormap (other than the color options available). people change the thresholds to get the nice pictures. Nick On Thu, 2008-12-04 at 19:50 -0800, Siddharth Srivastava wrote: > Hi everyone, > while the machine is busy crunching through our > data set, i would > like to prepare myself from the next step of the analysis, which is a > region-wise > analysis of the computed metrics by the freesurfer pipeline. Being a > complete > novice in the use of this software, i would like to know how do i go > about > doing the following: > > 1) With the parcellations already available in freesurfer, i would > like to > extract metrics (curvature, lgi, thickness) etc. for each label, > and > process them outside freesurfer (matlab, since i am more used to > it). Is it possible to do this within freesurfer or without, i.e > read these > values on the pial/white matter/inflated surfaces, ans also > extract ones > corresponding to a particular label? > 2) How do i go about generating a group average of the various maps > that freesurfer generates (curvature/thickness/lgi) ? As i > understand, > the analysis is done entirely in the subject space. Can i apply a > transformation > to the generated surfaces for averaging? Or does it require a re- > processing > after registering/reslicing all the data to a common space? > 3) I am still struggling with a proper colormap, which can bring out > the structure in out data. I see very nice renderings in > various > publications, of data generated with freesurfer. Is it possible > to tweak > the colormap to get such a rendering? > > Thanking you all in anticipation, > sid. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
