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 <nicks@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
> <nicks@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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