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
what files did it create? Please submit this as a separate question, too
hard to follow with all this other stuff.
>
>
>
> > 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.
If you want to use a different subject, you need to spec the surface
registration for that subject and that subject as a target. If you only
spec --target and the target is an average you have created with
make_average_subject, then it is effectly the same as just using
fsaverage because the registration to fsaverage is used.
>
> 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?
yes
>
> 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
It might be a version problem. You can create a symbolic link from
lh.white_avg to lh.white
> _________________________
>
> 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
Phone Number: 617-724-2358
Fax: 617-726-7422
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