I want to ask a related question: We study group differences between patients
and controls, and correlations of symptoms and thickness in patients only. We
would like to display (and extract) the common regions between two analyses in
ONE figure. Which template can we use?
We created two sets of ROIs in Qdec: one set is defined using an averge from
all subjects; the other set is defined using an average of patients only. The
ROI.labels from one set can not be loaded correctly on the average tamplate of
the other set. The problem remains even if we convert both sets of ROI.labels
to individual spaces. can we use fsaverage for both analyses?
thanks,
Xin Wang
________________________________
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 1/5/2009 2:23 PM
To: Siddharth Srivastava
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] questions about region-wise analysis data
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> 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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> >
> >
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