31 Mar
2014
31 Mar
'14
3:08 p.m.
Looking in the command window, qdec seems to only produce mri_glmfit (but not mri_glmfit-sim) commands, which is probably why the file you mention is not being produced in my case
On 31 March 2014 20:55, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
That is weird. the easiest thing is to just run mri_glmfit-sim using the same parameters as qdec is using. You can probably even get the command-line from the terminal window doug
On 03/31/2014 02:39 PM, Tudor Popescu wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto: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> > <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 <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 > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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> > <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
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> > > > _______________________________________________ > > 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 > > > > > > > > > > _______________________________________________ > > 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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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> > <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 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>
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