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 threadhttps://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 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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