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 <gr...@nmr.mgh.harvard.edu > <mailto: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 > <mailto: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 <mailto:gr...@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. > > > > > _______________________________________________ > 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
