On 31 March 2014 19:07, Douglas N Greve <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>> 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>>> 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
> > >
> > >
> > > _______________________________________________
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu

> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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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>>

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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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