On 2 April 2014 00:15, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

On 04/01/2014 05:48 PM, Tudor Popescu wrote:

Hi Doug

I did, however did not see an explanation as to exactly which folder 'glmdir' represents; the designName folder made the most sense to me. It seems, however, the error was with the 'abs' term anyway.

It should the the designName folder (it will have a mri_glmfit.log file).

Your mri_glmfit-sim command line is not correct and does not match examples in the help. Basically you need to spec "--cache 1.3 abs" not "--cache 1.3 --sim-sign abs"

Thanks Doug, now it worked, however I'm getting this error, which several other people seem to get: "Computing spatial average of each frame
0 1 2*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e8df328 ***". I am running FS 5.3.0 through VirtualBox, 2GB ram allocated.

Also, just for reference, the following command was straight out of the --help examples:
mri_glmfit-sim --glmdir lh.thickness.sm05 --cache 3 --sim-sign pos

..and since it is an 'example' rather than a 'syntax', one would assume that the --sim-sign was to be used as such, rather than having to be user-replaced

There is a clusterwise correction section in the viewing tab

Yes, that's where I ran the MC-Z from which showed me the sig clusters that I want to extract values from - should /that /have created the y.ocn.dat file? When I press Run there, it is a "mri_surfcluster" command that's launched, and not mri_glmfit-sim.

Yes, I see that now. I thought it was running mri_glmfit-sim, which would have made it easier for everyone.

Phew, I was starting to think I'm missing something very obvious! Yes this would indeed be a useful feature, in case you will have a chance to implement it in future versions.

doug

On 1 April 2014 23:39, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Did you look at the mri_glmfit-sim --help yet?

On 04/01/2014 04:42 PM, Tudor Popescu wrote:

Sorry I know that our questions often have an answer in the
documentation, but this case does not seem straightforward. I
ran the following command
mri_glmfit-sim --glmdir
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --cache
1.3 --sim-sign abs
..from either $SUBJECTS_DIR, the qdec folder, and the design
name folder - but in all cases I get errors such as "Flag abs
unrecognized."

I assume glmdir is the folder that QDEC creates with the
DesignName that I set.

Doing this from qdec would be easier so hopefully there is a
way to do that instead.
Thanks!

On 1 April 2014 22:25, Tudor Popescu <tudor3@gmail.com
<mailto:tudor3@gmail.com> <mailto:tudor3@gmail.com
<mailto:tudor3@gmail.com>>> wrote:

Thanks Doug. I found older threads where you advise that
csdbase.y.ocn.dat can also be produced by running the
simulation
from QDEC, but I didn't see any options for that in QDEC
1.5 (FS
5.3.0), after selecting my contrast and running the
correction -
how can this be done?
Thanks!

On 1 April 2014 20:37, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

Yes, run mri_glmfit-sim from the command line
doug

On 04/01/2014 02:26 PM, Tudor Popescu wrote:

Hi Doug

Apologies to insist, I just wasn't sure whether
you'd seen
my reply. To recap, qdec only used mri_glmfit (not
mri_glmfit-sim) in my case, so I don/t have any
*y.ocn*
files. Can I still extract values from my clusters?
Many thanks again
Tudor

On 31 March 2014 21:08, Tudor Popescu
<tudor3@gmail.com <mailto:tudor3@gmail.com>
<mailto:tudor3@gmail.com
<mailto:tudor3@gmail.com>> <mailto:tudor3@gmail.com
<mailto:tudor3@gmail.com>
<mailto:tudor3@gmail.com
<mailto:tudor3@gmail.com>>>> wrote:

Looking in the command window, qdec seems to
only produce
mri_glmfit (but not mri_glmfit-sim) commands,
which is
probably
why the file you mention is not being produced
in my case

On 31 March 2014 20:55, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

That is weird. the easiest thing is to
just run
mri_glmfit-sim
using the
same parameters as qdec is using. You can
probably
even get the
command-line from the terminal window
doug

On 03/31/2014 02:39 PM, Tudor Popescu wrote:
> Yes, in qdec I selected .05 for Monte-Carlo
Null-Z and ran the
> correction, which created the
mc-z.abs.th13.*
files (but no
y.ocn). I
> repeated the analysis just now - same
result.
>
>
> On 31 March 2014 20:13, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:
>
>
> And did you run the clusterwise
correction
for multiple
comparisons?
> Either from qdec or with mri_glmfit-sim?
That y.ocn file
should be
> there
>
> On 03/31/2014 02:02 PM, Tudor
Popescu wrote:
> > 5.3.0
> >
> >
> > On 31 March 2014 19:07, Douglas N
Greve
> <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
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> <mailto:greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote:
> >
> >
> > what version of FS are you running
> >
> >
> > On 03/31/2014 12:48 PM, Tudor
Popescu
wrote:
> > > Hi Doug
> > >
> > > The only OCN files I have in
my qdec
correlation
contrast
> folder
> > > (after having run the MC-Z
correction) are
> > mc-z.abs.th13.sig.ocn.annot
> > > and mc-z.abs.th13.sig.ocn.mgh.
> > >
> > > How should I obtain
mc-z.abs.th13.y.ocn.dat, and
what command
> > (if not
> > > mri_glmfit-sim) should I use
on it
in order to
extract values
> > from the
> > > two clusters?
> > >
> > >
> > >
> > > On 31 March 2014 18:35,
Douglas N Greve
> > <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>>>>
> <mailto:greve@nmr.mgh.harvard.edu
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> > >
<mailto:greve@nmr.mgh.harvard.edu
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> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
> > <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>>> wrote:
> > >
> > >
> > > The file you are looking for
should be
something like
> > > mc-z.abs.th13.y.ocn.dat
> > > you dont need to run
mri_glmfit-sim again
> > >
> > > On 03/31/2014 12:25 PM,
Tudor
Popescu wrote:
> > > > Thanks Doug,
> > > > Presumably that file is
mc-z.abs.th13.pdf.dat, which
> gets
> > created
> > > > after running the null-z
correction.
> > > > Based on the --help
and on a
previous thread
> > > >
> > >
> >
> <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html>,
> > > > I gathered it's this
command
that I need:
> > > > mri_glmfit-sim --glmdir
mc-z.abs.th13.pdf.dat
> > --cache 1.3
> > > > --sim-sign abs
> > > > I ran it from the
SUBJECTS_DIR
folder, the
design folder
> > or the
> > > > contrast folder
(lh-Avg-pial_thickness-score-Cor),
> but in all
> > > cases it
> > > > says "ERROR: cannot find
mc-z.abs.th13.pdf.dat"
> > > > Is this really the
command I
need to
simply extract the
> > values from
> > > > the 2 clusters found
in the
analysis?
> > > > THanks again
> > > > Tudor
> > > >
> > > >
> > > > On 31 March 2014 17:44,
Douglas N Greve
> > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>>>> wrote:
> > > >
> > > >
> > > > If you ran the clusterwise
correction,
then
> there will
> > be an
> > > > output file
> > > > with the data you want
already
there. Run
> mri_glmfit-sim
> > > --help to get
> > > > more info
> > > > doug
> > > >
> > > > On 03/31/2014 11:28
AM, Tudor
Popescu
wrote:
> > > > > Dear Freesurfer experts,
> > > > >
> > > > > After a qdec
contrast that asked
where does
> thickness
> > > correlate with
> > > > > behavioural score, I
got 2
significant
> clusters, and
> > I would
> > > > like, for
> > > > > each of these
clusters, to
have a
list of
> extracted
> > average
> > > > thickness
> > > > > values (across the
entire
cluster),
for each
> subject
> > that
> > > I can then
> > > > > plot externally
against the
score
values.
> > > > >
> > > > > I tried applying
answers to
previous
similar
> > questions with no
> > > > > success; some of them
suggested using
> mri_segstats,
> > > however I'm not
> > > > > very clear on how
annotation
files
are to be used
> > (I've only
> > > > used the
> > > > > QDEC GUI), and I
wasn't able
to work
out the
> syntax
> > that would
> > > > give me
> > > > > what I wanted (assuming
mri_segstats
is in
> fact the
> > command to
> > > > be used)
> > > > >
> > > > > Thanks for any help!
> > > > >
> > > > > Best wishes,
> > > > > Tudor
> > > > >
> > > > >
> > > > >
_______________________________________________
> > > > > Freesurfer mailing list
> > > > >
Freesurfer@nmr.mgh.harvard.edu
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> > > > >
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > > --
> > > > Douglas N. Greve, Ph.D.
> > > > MGH-NMR Center
> > > >
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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