On Sat, Feb 04, 2006 at 07:07:28AM +0000, Steve Smith wrote:
> Errr....the final maths I'm guessing, as those numbers that you sent
> _do_ give about 1% when multiplied together according to your
> (correct) equation......?
>
> Cheers, Steve.
Aah, uuhh, well, I think I somehow confused the value with a
peak/baseline relation. Yes, that must be true. Everything else is too
embarrassing.
Anyway, thanks for your help and sorry for the noise on the list.
Bye,
Michael
>
>
> On 2 Feb 2006, at 11:55, Michael Hanke wrote:
>
> >On Wed, Feb 01, 2006 at 07:34:04AM +0000, Steve Smith wrote:
> >>Hi - sure, sounds like the best thing to do is to create an image
> >>containing the % changes values and then use avw2ascii or probably
> >>better avwmeants -showall.
> >>
> >>First create the temporal mean of filtered_func_data using -Tmean in
> >>avwmaths
> >>
> >>If you take the relevant pe image from the .feat/stats directory, and
> >>divide by the mean and * by 100 you'll get what you want as long as
> >>the model was of height 1 - more more details you might want to look
> >>at the featquery TCL source code.
> >Thanks for the hint.
> >
> >I tried the simple way, but got far too high signal changes (>5%).
> >Obviously my model was not of height 1. So I looked in the featquery
> >code to see what has to happen.
> >
> >The procedure is the following (correct me if I'm wrong):
> >
> >1. Calculate the temporal mean of the functional volumes.
> >2. Get the model height from design.mat
> > grep PPheights design.mat | awk '{ print $2 }'
> >3. Calculate: (PE1 image) * (model height) * 100 / (temporal mean)
> >
> >If I got that right, something else must be wrong. Because, If I
> >look at the
> >tsplot output graph for a certain voxel I see a fairly good model fit.
> >Baseline is something about 10300 and peakvalue slightly above 10400
> >which gives approx. 1% signal change.
> >
> >The above method gives 39% for the same voxel instead.
> >PE: 382.161
> >PPheight: 3.748712e-01
> >TMean: 10302.1
> >
> >
> >What am I doing wrong?
> >
> >I'm using a Gamma convolution with added temporal derivative in FEAT.
> >
> >
> >
> >Cheers,
> >
> >Michael
> >
> >
> >>On 31 Jan 2006, at 11:32, Michael Hanke wrote:
> >>
> >>>Hi!
> >>>
> >>>I need to calculate an estimation of the % signal change of a large
> >>>number of (individual) voxels for several individual stimulus onsets
> >>>(event related design).
> >>>
> >>>I tried the following procedure:
> >>>
> >>>1. Slicetiming and motion correction of the functional volumes.
> >>>2. Highpass and lowpass filtering.
> >>>3. Extract a range of volumes around a single stimulus onset
> >>> (from 5 volumes before stimulus onset till 25 volumes after
> >>> stimulus offset).
> >>>4. Mask extracted functional dataset with ROI mask.
> >>>5. Run feat on the dataset (square-wave stimulus modell with
> >>>onset on
> >>> the 5. volume).
> >>>
> >>>As I see it, I have two possibilities now: The exact way would be
> >>>to use
> >>>featquery for each voxel in my ROI (because I need the signal
> >>>change in
> >>>each voxel individually and not in the ROI mask as a whole). But
> >>>this
> >>>his some disadvantages for me. a) it takes a long time b) I need to
> >>>extract the signal change value from an HTML file (or are they
> >>>available
> >>>somewhere else?).
> >>>
> >>>Because I want to process ALL signal change values toghether with a
> >>>script
> >>>I was looking for a way to get them a little easier. I tried using
> >>>tsplot for every voxel in the ROI and calculated % signal change
> >>>from
> >>>the tsplot timeseries output for the full model. This works quite
> >>>well,
> >>>altough it is not as exact as the previous procedure. But it still
> >>>takes
> >>>some time.
> >>>
> >>>Is there a faster or easier way to get the sigbal change in
> >>>individual
> >>>voxels?
> >>>
> >>>Thanks in advance.
> >>>
> >>>
> >>>Michael
> >>>
> >>>
> >>>--
> >>>GPG key: 1024D/3144BE0F Michael Hanke
> >>>http://apsy.gse.uni-magdeburg.de/hanke
> >>>ICQ: 48230050
> >>
> >>
> >>---------------------------------------------------------------------
> >>---
> >>------------------
> >>Stephen M. Smith, Professor of Biomedical Engineering
> >>Associate Director, Oxford University FMRIB Centre
> >>
> >>FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> >>+44 (0) 1865 222726 (fax 222717)
> >>
> >>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >>---------------------------------------------------------------------
> >>---
> >>------------------
> >
> >--
> >GPG key: 1024D/3144BE0F Michael Hanke
> >http://apsy.gse.uni-magdeburg.de/hanke
> >ICQ: 48230050
>
>
> ------------------------------------------------------------------------
> ------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ------------------------------------------------------------------------
> ------------------
--
GPG key: 1024D/3144BE0F Michael Hanke
http://apsy.gse.uni-magdeburg.de/hanke
ICQ: 48230050
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