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 <gr...@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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 > > > 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. > >
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