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> 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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