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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