Sid, A group analysis can be performed from the command-line using mri_glmfit directly. See this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis You can use a different average subject, other than fsaverage, although it doesnt improve an analysis to use a subject from your group. Also, you can create a symlink from $FREESURFER_HOME/subjects/fsaverage to your SUBJECTS_DIRS, to spare having to copy the data. Nick On Sun, 2008-12-28 at 12:01 -0800, Siddharth Srivastava wrote: > Hi Nick, > Thanks, It was my mistake. It works exactly as you say. > I still have to look at qdec documentation, but could i ask if it is > possible to perform the group analysis in a batch mode, without > the GUI, i.e ? > > regarding the movement of data, the first time i did it, i got a > screen full > of memory addresses and corresponding routines, followed by a crash ( > exit from wish, back to shell). I am not able to replicate it, seems > to work > now. > > Also, is it possible to register everything to a different surface, > other > that fsaverage.. for example to one of the subjects? Can this be > located > outside the relative paths reachable via $SUBJECTS_DIR ? In fact, can > fsaverage be located outside? For the processing i did, i had to copy > the fsaverage as one of the subjects, so that it can be located > within > the current context of $SUBJECTS_DIR . > > Thanks again, for the timely help. > sid. > > > On Sun, Dec 28, 2008 at 9:17 AM, Nick Schmansky > <ni...@nmr.mgh.harvard.edu> wrote: > Sid, > > The .mgh files, in the case of the commands you ran, store > surface data > corresponding to the 'fsaverage' subject. So you would first > load the > inflated surface for fsaverage (tksurfer fsaverage lh > inflated), then > you would use the Load Overlay menu option to load the .mgh > file(s) you > created. You probably will have to adjust the color > thresholds (View- > >Configure->Overlay). For the lgi data, you can use: > > recon-all -s subj -qcache -measure pial_lgi > > which will sample the subjects lgi data to the fsaverage > surface, at > which point you could average that (although typically a > statistical > analysis is performed on the set of subjects sampled to > fsaverage, see > out group analysis slides and tutorial pages). > > You should be able to move subject data around to other > directories > without any problems. Does tksurfer really halt after that > 'not in > scripts dir' message? That is a common message and not an > error. Can > you open tksurfer for the sample bert subject? > > Nick > > > > > On Sat, 2008-12-27 at 19:14 -0800, Siddharth Srivastava wrote: > > Hi Nick, > > I finally got a chance to use the sequence of > command > > that you had provided below. In continuation of this thread: > > > > a) The output of using the command mentioned in reply 2) > below > > is an MGH file (and not faces/vertices combination)? How is > it > > possible to get a smoothed surface > > that i can load as an overlay in tksurfer? I would > ultimately > > like to average all the smoothed lgi mappings as one single > > surface per hemisphere. Is this possible in freesurfer? In > any case, > > although > > my pial_lgi surfaces look ok, i do not see anything in > > the .fwhmxx.fsaverage.mgh files, when > > i load them using tkmedit. what can be going wrong? I used > fwhm = > > 15. > > > > b) Are there known issues with migrating the data set > processed > > partiallty > > at one mount point, to some different location? Due to lack > of space, > > i had to do some recon-all processing in one directory, and > then > > copied the tree to a different > > location for subsequent steps. I get tksurfer errors > "surfer: not in > > "scripts" dir ==> using cwd for session root", > > followed by, what i think, a read attempt of the > corresponding T1.mgz > > file. No window is drawn. > > I googled with the error string, and it seems there was a > similar > > error under discussion, which > > had to do with moving files and absolute paths. I was not > able to > > understand the fix, though, > > and hence i wanted to confirm with the list what exactly has > to be > > done in this situation. > > > > Thanks, > > sid. > > > > On Fri, Dec 5, 2008 at 10:42 AM, Nick Schmansky > > <ni...@nmr.mgh.harvard.edu> wrote: > > 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 > > > > _______________________________________________ > 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
