Yes, in qdec I selected .05 for Monte-Carlo Null-Z and ran the correction, which created the mc-z.abs.th13.* files (but no y.ocn). I repeated the analysis just now - same result.
On 31 March 2014 20:13, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > And did you run the clusterwise correction for multiple comparisons? > Either from qdec or with mri_glmfit-sim? That y.ocn file should be there > > On 03/31/2014 02:02 PM, Tudor Popescu wrote: > > 5.3.0 > > > > > > On 31 March 2014 19:07, Douglas N Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > what version of FS are you running > > > > > > On 03/31/2014 12:48 PM, Tudor Popescu wrote: > > > Hi Doug > > > > > > The only OCN files I have in my qdec correlation contrast folder > > > (after having run the MC-Z correction) are > > mc-z.abs.th13.sig.ocn.annot > > > and mc-z.abs.th13.sig.ocn.mgh. > > > > > > How should I obtain mc-z.abs.th13.y.ocn.dat, and what command > > (if not > > > mri_glmfit-sim) should I use on it in order to extract values > > from the > > > two clusters? > > > > > > > > > > > > On 31 March 2014 18:35, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > > > > 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> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto: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> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto: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> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto: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> > > > <http://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> > > > <http://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> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto: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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto: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> > > <mailto: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> > > > <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> > > > <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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > _______________________________________________ > > 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 >
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