Hi all,
I am trying to understand the --surf flag in the mri_glmfit
command, and the 2 parameters that follow it. The tutorial mentions
--surf average lh .
1) what should "average" contain? should it point to the average of
the population, of fsaverage, or is it just a flag?
2) lh: is this just the specification of the hemisphere to be processed
or should it point to a valid set of files.
If i am doing a group analysis of a measure (say, thickness), and i have
smoothed thickness maps registered to a population specific template in
a subdir, how should i specify --surf and subsequebt parameters?
Further, i also get an error saying --C command not found (for the contrast
vector).
why is this happenning?
best regards,
sid.
On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky
<ni...@nmr.mgh.harvard.edu>wrote:
> 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.
> > >
> > > > _______________________________________________
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> > >
> > >
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