Hi Eugene, Steve, and others,
Perhaps I'm missing it from the command line syntax, but there an easy
way to use your 'setFEAT' script to generate say a higher-level design
for a repeated measures design involving say 87 subjects each with 4
repeats (to borrow from a recent design posted to the list that was
causing problems via the GUI).
Or more broadly, is there any tool or mechanism that allows one to
convert simple text files containing matrices/vectors with contrast and
design matrix specifications (e.g., simple matlab-generated precursors
to the .con and .mat files, without the /NumWaves, /PPheights, etc
stuff) and then transform those files into a proper .fsf file, without
ever having to cut/paste a design within the GUI itself? That way, one
could avoid the GUI entirely when working with large designs (e.g.,
repeated measures designs with many subjects; or FIR models involving
numerous response types and thus many EVs). If not, the ability to
directly supply the contrast and design matrix specifications, and have
FEAT work out all the other stuff automatically would be a VERY useful
capability.
Relatedly, I'm puzzled by the relationship between the .con, .mat,
and .fsf files, since the .fsf files redundantly code the contrast and
design matrix in a very text intensive format. How do those 3 files
work together, and what happens in the event of conflicting information
between them?
thanks,
-MH
On Thu, 2011-05-26 at 10:57 +0100, Eugene Duff wrote:
> Hi Erie -
>
>
> It's quite common to have a few copes per subject, but 30 per person
> is not that common, so it wasn't expected that having to run separate
> top-level analyses would be that laborious (particularly if using the
> paste option to enter the cope dirs from an ls command).
> Automatically reading all cope.feats within supplied gfeat directories
> would add a bit of complexity to the coding I think, producing gfeats
> within gfeats.. The error on the webpage is being corrected
> ("subjectN.gfeat/" right?), thanks. Let me know if anything is
> unclear..
>
>
> I've got a basic bash script setFEAT which might make scripting a bit
> easier for some things (attached, but be sure to check it's doing what
> you expect).
>
>
> Cheers,
>
>
> Eugene
>
>
>
> On 25 May 2011 22:06, Michael Harms <[log in to unmask]> wrote:
> Yes, AFAIK you can only run one lower level cope at a time
> with the
> approach that I suggested, so you either need to script it (as
> you did)
> or just do it manually if there are not too many.
>
> cheers,
> -MH
>
>
> On Wed, 2011-05-25 at 13:48 -0700, Erie Boorman wrote:
> > Hi Michael,
> >
> >
> > I selected the option "inputs are lower-level FEAT
> directories". I
> > could see how this approach would work if I only had 1 cope
> per
> > subject. The issue is that one often has multiple copes per
> subject
> > (e.g. I have 30 copes per subject).
> >
> >
> > Just to clarify, I have come up with a workable solution,
> which is to
> > run a separate FEAT analysis per cope (I set up the
> design.fsf file
> > for one cope and then run a script that runs the analysis
> across copes
> > by changing the cope number). This works just fine but it is
> not very
> > user-friendly and also seems somewhat inefficient. Further,
> it seems
> > that the instructions on the feat webpage are incorrect. I
> would
> > imagine that a similar issue will be encountered by anyone
> who has
> > many copes per subject and multiple runs per subject, which
> seems
> > quite common.
> >
> >
> > Best,
> > -Erie
> >
> > On Wed, May 25, 2011 at 1:35 PM, Michael Harms
> > <[log in to unmask]> wrote:
> > Hi Erie,
> > What format did you use for specifying your "lower-
> level FEAT
> > directories" for your Lev3 analysis?
> >
> > If you use something like:
> > path_to_S1.gfeat/cope1.feat
> > path_to_S2.gfeat/cope1.feat
> > path_to_S3.gfeat/cope1.feat
> > path_to_S4.gfeat/cope1.feat
> > ...
> >
> > it should work just fine.
> >
> > cheers,
> > -MH
> >
> >
> > On Wed, 2011-05-25 at 12:50 -0700, Erie Boorman
> wrote:
> > > Hi Eugene,
> > >
> > >
> > > Yep, you've got it right. I have thirty separate
> first level
> > copes for
> > > each of four sessions and have ten subjects.
> Following the
> > > instructions on the FSL webpage to the best of my
> ability, I
> > first
> > > tried the following:
> > >
> > > 1) Ran a lower-level FEAT for each run for each
> subject.
> > >
> > > 2) Constructed a higher-level FEAT where the
> inputs were
> > lower-level FEATs for each run for each subject
> (i.e. 40 FEATs
> > corresponding to 40 runs). In the stats tab, I
> selected the
> > Fixed Effects option and set up the design with 40
> EVs, where
> > each EV picks out the 4 sessions that correspond to
> a
> > particular subject. I also included 10 contrasts to
> represent
> > the 10 subject means.
> > >
> > > Rather than output something like
> > subject_N.gfeat/cope1.feat, this second level
> analysis output
> > 30 cope.feat directories, each with 10 cope.nii.gz
> files in
> > its stats directory. The file structure was as
> follows:
> > Group_Ana/cope[n].feat/stats/cope[j], where n = 1:30
> lower
> > level contrasts and j = 1:10 subjects. This is
> different from
> > what the instructions implied would be output.
> > >
> > > Next, I followed some other FSL users' advice (and
> my
> > intuition). After completing step 1 above I:
> > > 1) Constructed a higher-level FEAT, using the
> fixed effects
> > option, across the four runs per subject for each
> subject.
> > > 2) Tried running a third level mixed effects
> analysis by
> > selecting each person's feat directory corresponding
> to the
> > fixed effects analysis across runs.
> > > When I set up the analysis, I receive the
> following warning
> > message after selecting the Feat directory
> corresponding to
> > the fixed effects analysis. I receive ten of these
> messages
> > (which corresponds to the number of subjects):
> > > Warning: the first selected Feat directory
> contains no
> > stats/cope images.
> > > This is most likely because there are thirty
> cope.feat
> > directories within the (.gfeat directory resulting
> from the
> > fixed effects analysis), each with a stats directory
> and a
> > single cope1.nii.gz within the stats directory. It
> seems to
> > fail because it cannot locate the stats directory
> within
> > the .gfeat directories.
> > > Cheers,
> > > -Erie
> > >
> > >
> > > On May 24, 2011, at 3:11 PM, Eugene Duff wrote:
> > >
> > > > Hi Erie -
> > > >
> > > >
> > > > What are the errors (if any) that you're getting
> when you
> > try the
> > > > approach described on the website? Could you
> see anything
> > in the
> > > > log files?
> > > >
> > > >
> > > > Have I got it right: you have thirty separate
> first level
> > copes for
> > > > each session and you'd ideally want to follow
> the multi-
> > session (4)
> > > > multi-subject (10) example for each?
> > > >
> > > >
> > > > Cheers,
> > > >
> > > >
> > > > Eugene
> > > >
> > > >
> > > > On 24 May 2011 21:56, Erie Boorman
> > <[log in to unmask]> wrote:
> > > > Hi,
> > > >
> > > > Thanks, Chris. I followed your
> instructions and
> > set up the
> > > > third-level analysis to be run for each
> cope
> > separately. I
> > > > ran this across copes using a bash
> script.
> > > >
> > > > While this worked fine it is hard for me
> to
> > believe that
> > > > there isn't a more automated way to do
> this? For
> > some
> > > > reason, simply running a third level
> mixed effects
> > analysis
> > > > with the FE results by selecting each
> person's
> > feat
> > > > directory so that the analysis is done
> on all
> > contrasts
> > > > simultaneously does not work for me
> either. This
> > would be a
> > > > lot more efficient/user-friendly. In
> case it's of
> > > > relevance, I'm using FSL 4.1 (2008).
> > > >
> > > > In any case, the instructions that are
> currently
> > specified
> > > > on the FSL webpage
> > > >
> >
> (http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#MultiSessionMultiSubject) listed under the section entitled Multi-Session & Multi-Subject (Repeated Measures - Three Level Analysis) appear to be incorrect. Given how common it is to conduct an analysis using multiple runs per subject, it would be very helpful if the webpage could be updated.
> > > >
> > > > Cheers,
> > > > -Erie
> > > >
> > > >
> > > >
> > >
> > >
> >
> >
> >
>
>
>
>
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