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
>
>
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