It depends on what you want the inputs to be at third level; quite
often any given third level analysis would only involve input from one
second-level .feat from each subject, and a separate third-level
analysis would take a different one, etc.
However, if you DO need to use all 100 as inputs then you can use the
"paste" function easily, along with an "echo" command in the terminal,
to paste the full list into the GUI without having to select all 100
separately.
Cheers.
On 1 Dec 2008, at 15:22, carlos silva pereira wrote:
> Hi Steve,
>
> thank you for your reply.
> I think I may be missing the point : I have 10 .feat directories
> (cope1.feat....cope10.feat) inside each subjects .gfeat directory,
> and I should select all of them as inputs? That means that, for my
> 10 subjects, I'll have to select 100 directories? Clearly I
> misunderstood what you explained...
>
> Best,
> Carlos
>
>
>
> 2008/12/1 Steve Smith <[log in to unmask]>
> Hi,
>
> I think the problem is just that your selected inputs to third level
> should be the .feat directories INSIDE the .gfeat second-level
> outputs, not the .gfeat directories themselves.
>
> Cheers.
>
>
>
> On 29 Nov 2008, at 17:22, carlos silva pereira wrote:
>
> Hello,
> I have a question related to the subject discussed bellow: I have
> done a first level Feat analysis for each of the 6 runs of my
> experiment, and then a FE analysis using as inputs the 6 first-level
> Feat directories.
> When I try to perform a third-level Flame1, feeding the gfeat
> directories as inputs, I get this "Warning: the first selected FEAT
> directory contains no stats/cope images", irrespective of the
> directory I choose first.
> What could be the problem, since the directories contain stats/cope
> images?
> Thanks in advance!
> Best
> Carlos
>
>
> 2008/11/13 Mark Jenkinson <[log in to unmask]>
> Hi,
>
> Just to add that we really do discourage the merging of timeseries
> data as it
> messes up the pre-processing - especially the temporal filtering.
> You are
> much better adding a separate level where you average over the runs
> using
> the GLM, with the first level just doing each run separately. This
> should be
> fine if you have 5 runs per subject. Have a look at the
> documentation at:
> http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#MultiSessionMultiSubject
> for more details.
>
> All the best,
> Mark
>
>
>
> On 12 Nov 2008, at 20:19, Eugene Duff wrote:
>
> Hi Yael,
>
> It is a bit unclear what you need to do. If you just want to do an
> typical single-subject multi-session analysis you probably do not
> need to manually merge your data. You run an ordinary first-level
> analysis on each session, then run a higher-level analysis in Feat,
> where you include each of the 1st level Feat directories as inputs.
> Feat then automatically merges the appropriate 1st level datafiles
> before it does the modelling. Otherwise, fslmerge is the tool to
> merge data.
> Eugene
>
>
> 2008/11/12 Yael Shani <[log in to unmask]>
> Hi Reza
> I'm not sure I understand. When you say merge do you mean the in the
> second level analysis feat takes all the runs and concatenate them
> into one long run or averages the results of all the runs?
> Thanks again
> Yael
>
>
> On Sun, Nov 9, 2008 at 5:45 PM, Reza Salimi <[log in to unmask]>
> wrote:
> Hi Yael,
> to merge some volumes, you can use fslmerge which does it in
> different directions(x,y,z,t)
> and also, in case of using a typical feat analysis, this merging
> happens itself as a part of the group-level analysis and
> merged result is saved as filtered_func_data.nii.gz
> hope it helps.
> cheers
>
>
> On Sun, Nov 9, 2008 at 3:39 PM, Yael Shani <[log in to unmask]> wrote:
> Hi FSL'rs
>
> I want to do a within subject analysis, but before I need to
> understand how to merge data.
> Each subject had 5 runs. I would like to treat these runs as one
> long session. How do I do that? As far as I understand the second
> level analysis with fixed effects does not concatenate. Am I right?
> Many thanks
> Yael
>
>
>
> --
> G. Salimi-Khorshidi,
> D.Phil. Student, Dept. of Clinical Neurology, University of Oxford.
> [log in to unmask] http://www.fmrib.ox.ac.uk/~reza
> FMRIB Centre, John Radcliffe Hospital,
> Headington, Oxford, OX3 9DU
> Tel: +44 (0) 1865 222466 Fax: +44 (0)1865 222717
>
>
>
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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