Thanks for for taking the time to take a look at this.
The code for the upload is:
129208
Marc
On Wed, Apr 21, 2010 at 3:49 AM, Stephen Smith <[log in to unmask]> wrote:
> Hi,
> Yes - we're not saying that the two approaches for the second-level FE
> modelling are exactly the same, just that there's no strong reason to choose
> one rather than the other and that they should generally be very close.
> On the other hand, I am a little confused by the strange dip in the
> histogram - could you upload the relevant .gfeat output directory so we can
> take a look?
> Please upload the files in a single compressed tarfile to
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> And then email me the upload ID.
>
> Cheers.
>
> On 20 Apr 2010, at 18:31, Marc Bouffard wrote:
>
> We keep getting a difference between the two ways at the second level.
> I have attached a sample subject 2nd level zstats map with
> histograms. The red-yellow part shows what is common between the 1
> subject model and the all subjects model. The blue part shows the
> extra activation from the 1 subject model which is mostly outside the
> brain. The top histogram is for the all subjects model and the lower
> one is the one subject model. Any ideas as to why the dip occurs from
> -2.5 to -2 on the lower histogram? This seems to occur in a
> consistent manner for all subjects we have analysed.
> (Sorry about the image quality but it has be under the 50k limit for
> FSL postings)
>
> Thank you,
> Marc
>
> On Mon, Apr 19, 2010 at 2:15 PM, Stephen Smith <[log in to unmask]> wrote:
>
> Hi, sorry that wording is a little confusing in the practical web page - a
>
> hangover from before we started recommending using FE. When you use FE
>
> the session-session variance is IGNORED, it's really just a pooling of the
>
> lower-level results, so that's why we're saying that it doesn't make a big
>
> difference which way the second-level is done in this case.
>
> Cheers.
>
>
>
>
> On 19 Apr 2010, at 14:29, Marc Bouffard wrote:
>
> Thank you for your reply. But it says in:
>
> http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/feat3/index.htm
>
> under:
>
> Group difference with multiple sessions for each subject
>
> that we should put all the second-level analyses into a single
>
> second-level model when there is a small number of runs for each
>
> subject because if we use one model/subject it would not lead to a
>
> good within subject session-to-session variance. So isn't that a
>
> strong reason to chose the single second-level model?
>
> Thanks again,
>
> Marc
>
> On Sun, Apr 18, 2010 at 12:21 PM, Stephen Smith <[log in to unmask]>
>
> wrote:
>
> Hi - yes, the two are not exactly the same, but I don't think there is a
>
> strong reason for choosing one versus the other.
>
> Cheers.
>
>
> On 14 Apr 2010, at 21:21, Marc Bouffard wrote:
>
> Hello,
>
> I think this has been covered in the forums before but I have not found a
>
> clear answer. What is the recommended way to combine/average fmri runs
>
> within subjects (following first-level analysis)? For example, if for each
>
> subject we have 2 fmri runs should we use the method outlined in one
>
> analysis/one model:
>
> http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#MultiSessionMultiSubject
>
> or should we have one separate model/analysis for each subject?
>
> I have tried both and get simlar results but the zstats from the latter are
>
> noisier particularly on the edges of the zstats images. So this suggests
>
> that the two are not doing exactly the same computations and therefore are
>
> not answering the averaging question in exactly the same way?
>
> Regards,
>
> Marc
>
>
>
> ---------------------------------------------------------------------------
>
> 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
>
> ---------------------------------------------------------------------------
>
>
>
>
> <2nd_level_test.rar>
>
> ---------------------------------------------------------------------------
> 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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