Our FSL version is 5.98
and the operating system is Ubuntu Linux 64 bit
Do you have any thoughts on what is causing the problem in the zstats histogram?
On Thu, Apr 22, 2010 at 12:12 PM, Stephen Smith <[log in to unmask]> wrote:
> Hi - we've looked into this and the results look fine here when we rerun
> flame - can you tell us what version of FSL you are running and what
> computer/OS you are using?
> Cheers.
>
>
>
> On 21 Apr 2010, at 14:44, Marc Bouffard wrote:
>
> 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
>
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
> ---------------------------------------------------------------------------
> 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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