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
> <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html>,
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
> 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:Freesurfer@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
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> Phone Number: 617-724-2358> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> 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
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing:> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> 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
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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer