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> 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 <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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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