Sorry, that read gender and age. The contrast takes age into account, it is just a problem with the code that generates the sentence. Have not had a chance to answer the others, I thought I'd try to get one wrapped up. It looks like you added a few more questions at the end. Unless they are closely related to the previous questions, can you send them separately, it is hard to keep track with all the replies to replies. doug
On 05/23/2013 02:51 PM, Tudor Popescu wrote: > Thanks Doug, however my question was why does QDEC not also display a > contrast to the effect of "Does the avg thickness, accounting for > *gender and age*, differ between group1 and group2?", instead it only > displays "Does the avg thickness, accounting for *gender*, differ > between group1 and group2?" > > Also, I was wondering whether you got a chance to see my other > questions from the same email.. > > Many thanks! > Tudor > > On 23 May 2013 17:49, Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > when I run qdec using your table and my data, I get a full > complement of contrasts, see attached. > doug > > > > > On 05/22/2013 01:43 PM, Tudor Popescu wrote: > > > > 1) In a design with group and gender as discrete > factors and age > > as a continuous factor, why is it that QDEC only > displays the > > contrast "Does the avg thickness, accounting for > gender, differ > > between group1 and group2?" and not also > "..acounting for gender > > and age,.."? > > > I thought that it would have. Are you coding age > as a nuisance > variable? > Also, are you coding gender as a continuous > variable? That is > something > you should not do. > > > I was not coding age as a nuisance variable but as a > continuous variable (co-variate). Gender was a > discrete/fixed > factor but I'm not sure whether this means > 'continuous' in the > sense discussed in your exchange with Arman. Anyway, > in this > configuration, it seems gender and age are not accounted > (controlled) for at the same time. > > It should be. Can you send your qdec table? > > See attached > > > > > 3) From the group tutorial, I see that > mris_preproc > has to be > > called with flag "--cache-in > ess.fwhm10thickn.fsaverage". > However, > > after running recon-all (including with the > –qcache > option) > on all > > my subjects, none of their folders contains > a file named > > ?h.thickness.fwhm10.fsaverage.mgh > > > Where does it say to use ess.fwhm10thickn.fsaverage? > > Sorry, typo. The flag is actually "--cache-in > thickness.fwhm10.fsaverage", I file that I do not have > after > having run recon-all (including with the --qcache option) > > Try running recon-all again with just the --qcache flag. > > This is what I had done previously; the command was: > recon-all -s C${i} -qcache > where the ${i} was a counter in a script, to run the command > on all my subjects > > > > > 5) What is the difference between running > make_average_subject and > > running mris_preproc with --target fsaverage? > > > make average subject makes the average subject. > mris_preproc > samples the > data into a common space defined by the registration > surface and > concatenates the input subjects into a single stack. > > But should the registration surface used by > mris_preproc (i.e. > its "--target" flag) come from the 'average' subject > or from > 'fsaverage'? In other words, which one of these > becomes the > study-specific template? > > You have to tell mris_preproc both the target and the surface > registration to use if you want to use a different > average subject. > > The command I used is: > > mris_preproc --fsgd group_gender__age.fsgd --target average > --hemi rh --meas thickness --out rh.thickness.mgh > > So if I understand correctly, the fact that I didn't indicate > a surface registration means that the surface from the > "average" subject will be used, rather than the one from > "fsaverage"? I still don't understand the difference between > those two, and which, if any, can be referred to as the > study-specific template. > > B) All concatenated volumes from mris_preproc's output > files > (?h.thickness.mgh) appear blank in freeview, even > though the > individual structurals all look fine. Also, > lh.thickness.mgh > and rh.thickness.mgh have, surprisingly, *exactly* the > same > file size, which is also a bit small (~25MB) to be able to > contain 38 registered structurals, which suggests > something > went wrong... > > These are surface overlay files, not volumes. You can't load > surfaces as volumes in freeview. > > So assuming I don't visually inspect the surface overlays, can > I assume that mris_preproc ran fine if lh.thickness.mgh and > rh.thickness.mgh have exactly the same file size? > > C) When running mri_surf2surf, I get an error saying > that file > /surf/lh.white cannot be opened. The 'average' folder > produced > after I ran make_average_subject does not contain a > /surf/lh.white file, only a /surf/lh.white_avg file! I > didn’t > find a log file from make_average_subject so i don’t > know if > it gave any errors.. > > It's extremely helpful to have command lines ... > > > Sorry, my commands were: > make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 > C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 > M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 > mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh > --fwhm 10 --tval lh.thickness.10.mgh > _________________________ > > Could someone please explain how the following descriptions of > a contrast are exactly linked: > i) a contrast's namesake folder (including keywords > 'Avg'/'Diff'/'X' and 'Intercept'/'Cor'; e.g. > "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure"), > ii) its phrasing in QDEC ("Does the thickness-age correlation > differ between group1 and group2?"), > iii) the assignment of values to each column of the design > matrix, in the C.dat contrast vector (e.g. [0, 0, 1, -1]) > > _________________________ > (this is actually a bug report) After setting a different FDR > threshold and pressing the "Set Using FDR" button, more often > than not the results image doesn’t change accordingly. I > noticed that the button only has an effect after moving around > the QDEC window and/or waiting a minute or so > > > -- > 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/ > > > > 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. > > -- 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
