On 31 March 2014 20:55, Douglas N Greve <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>> 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
> <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>>

> > > <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>>
> > <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:
> > > >
> > > >
> > > > 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
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > > >
> > 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>
> > <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>>>>
> > > > Phone Number: 617-724-2358
> > > > Fax: 617-726-7422
> > > >
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> > > >
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> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > 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>>>
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
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> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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