Siddharth Srivastava wrote:
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?
This is the name of the average subject as created by
make_average_subject. If you did not make an average subject, then use
fsaverage.
2) lh: is this just the specification of the hemisphere to be processed
or should it point to a valid set of files.
Just the hemisphere
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?
The input is specified with with --y. The --surf just tells glmfit that
it is a surface so that it can compute the FWHM appropriately.
Further, i also get an error saying --C command not found (for the
contrast vector).
why is this happenning?
Can't say without the cmd line, but I'm guessing you have a rouge space
in your script
best regards,
sid.
On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky
<ni...@nmr.mgh.harvard.edu <mailto: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 <mailto: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
<mailto: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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> >
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