Hi Alina,
I was not suggesting to compute this ratio for all of your images but
only for the beta images from the GLM, ie a single call to ImCalc:
spm_imcalc({'beta_0001.nii','beta_0002.nii'},'psc.nii','i1./i2');
Best regards,
Guillaume.
On 11/04/17 14:39, Alina D wrote:
> Hello,
>
> Thank you very much! I did try adjusting the threshold and the constant
> predictor is not looking weird anymore when I set it to 0.9.
> Nevertheless the beta values that I am getting are still quite high. I
> would like to also try your initial suggestion of dividing the images by
> the mean image (if I understood it correctly)/ I computed the mean image
> with ImCalc but now I run into (I think rather easy but I don't know how
> to do it) problem. Is it possible to divide each of all my 60 images by
> the mean image using ImCalc?
>
> Best wishes,
> Alina
>
> On Mon, Apr 10, 2017 at 6:12 PM, Guillaume Flandin <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear Alina,
>
> There indeed seems to be a lot of variability in intensity over space in
> your images so you might want to reduce the value of the masking
> threshold (defaults.mask.thresh in spm_defaults.m, see an earlier
> message today for further details) before model specification.
> You sent me the SPM.mat from the model with iid assumptions (serial
> correlation: none) so I couldn't check the temporal covariance
> structure.
> If you want to get local estimates of the percent signal change, you can
> compute the ratio beta_1/beta_2 (use ImCalc with images beta_0001.nii
> and beta_0002.nii and expression 'i1./i2'), see this for details:
>
> http://journal.frontiersin.org/article/10.3389/fnins.2014.00001/full#h6
> <http://journal.frontiersin.org/article/10.3389/fnins.2014.00001/full#h6>
>
> Best regards,
> Guillaume.
>
>
> On 05/04/17 16:30, Alina D wrote:
> > Hello,
> > I ve been trying mucltiple times to send the files to you but the
> > mailling lists rejects it. I hope this works.
> >
> > Thank you,
> > Alina
> >
> > On Tue, Apr 4, 2017 at 6:14 PM, Guillaume Flandin <[log in to unmask] <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
> >
> > Dear Alina,
> >
> > The change in the design matrix between before and after
> estimation is
> > due to non-sphericity whitening (adjusting for serial
> correlations). In
> > your case, it seems it went wrong - to understand better what
> is going
> > on, could you rerun your entire analysis while setting the "serial
> > correlations" option in fMRI model specification to "none"?
> > Also, what does your difference images look like? Before
> entering the
> > GLM, the data are rescaled according the estimated global
> signal, and
> > this estimation is based on a crude intensity thresholding
> approach to
> > define the brain mask. What does the mask.nii image look like?
> >
> > Best regards,
> > Guillaume.
> >
> >
> >
> > On 04/04/17 16:18, Alina D wrote:
> > > Hello,
> > >
> > > These are actually arterial spin labelling difference
> images, so the
> > > only processing was smoothing them by 6mm. Then I specified
> everything
> > > by clicking on the specify first level command. What I
> noticed is that
> > > after I am doing this step, indeed the " clean" design
> matrix (that I
> > > just send before) comes up. Nevertheless, after model
> estimation and in
> > > the results file the design matrix looks again like the
> initial one,
> > > with the odd looking constant term. Could this be the source
> of error?
> > > And if yes, why is this happening?
> > >
> > > Best wishes,
> > > Alina
> > >
> > > On Apr 4, 2017 5:04 PM, "Guillaume Flandin"
> <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>> wrote:
> > >
> > > Dear Alina,
> > >
> > > Your design matrix looks better this time: it contains two regressors
> > > (task and constant) so you have two regression coefficients beta_1 and
> > > beta_2. You are right to find the values rather large.
> > > Where are the data coming from? How did you preprocess them? Did you use
> > > SPM's batch interface to specify and estimate this first level GLM?
> > >
> > > Best regards,
> > > Guillaume.
> > >
> > >
> > > On 04/04/17 12:54, Alina D wrote:
> > > > I apologize, I selected the wrong file accidentally.
> > > > These are the betas. Could you please tell me what is the first
> > > one and
> > > > what is the second one?
> > > > beta =
> > > >
> > > > 134.8669
> > > > 196.3979
> > > >
> > > > And this is the correct design matrix :
> > > >
> > > > Inline image 2
> > > >
> > > > Best wishes,
> > > >
> > > > Alina
> > > >
> > > > On Mon, Apr 3, 2017 at 5:45 PM, Guillaume Flandin
> > > <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>> wrote:
> > > >
> > > > Dear Alina,
> > > >
> > > > Your second regressor, the constant term, looks odd. How did
> > > you specify
> > > > your GLM?
> > > >
> > > > Best regards,
> > > > Guillaume.
> > > >
> > > > On 03/04/17 16:38, Alina D wrote:
> > > > > Hello,
> > > > >
> > > > > Thank you again. This is how the design matrix looks like. I
> > > only have
> > > > > one stimulation condition.
> > > > > Best wishes,
> > > > > Alina
> > > > > Inline image 2
> > > > >
> > > > > On Mon, Apr 3, 2017 at 5:29 PM, Guillaume Flandin
> > > <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>
> > > > > <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>>> wrote:
> > > > >
> > > > > Dear Alina,
> > > > >
> > > > >
> > > > > OK, you probably read the data correctly. Could
> > you show us
> > > > what your
> > > > > design matrix look like? To explore a bit
> further,
> > you can
> > > > also use the
> > > > > "plot" button with the "contrast estimates" and
> > "fitted
> > > responses"
> > > > > options.
> > > > >
> > > > > Best regards,
> > > > > Guillaume.
> > > > >
> > > > >
> > > > > On 03/04/17 16:20, Alina D wrote:
> > > > > > Hello,
> > > > > >
> > > > > > Thank you very much for replying. I did
> Extract
> > data >
> > > betas
> > > > > this
> > > > > > voxel and the only thing that happens is
> that matlab
> > > returns
> > > > this :
> > > > > >
> > > > > > beta =
> > > > > >
> > > > > > 87.2718
> > > > > > 265.9859
> > > > > >
> > > > > > Before I tried to load the beta_0001.nii
> file and to
> > > get the
> > > > intensitied
> > > > > > of some voxels from there.
> > > > > >
> > > > > > Qse = 'beta_0001.nii';
> > > > > > Wse = spm_vol(Qse);
> > > > > > Bse = spm_read_vols(Wse);
> > > > > >
> > > > > > I stored the coordinates of the voxels in a
> > matrix of
> > > the form:
> > > > > > myindex3d = zeros(length(myindex),3)
> > > > > >
> > > > > > And then looped through the total number and
> > ploted it :
> > > > > > scatter_data(ii) =
> > > > Bse(myindex3d(ii,1),myindex3d(ii,2),myindex3d(ii,3))
> > > > > >
> > > > > > What would you suggest?
> > > > > >
> > > > > > Best wishes,
> > > > > > Alina
> > > > > >
> > > > > > On Mon, Apr 3, 2017 at 5:05 PM, Guillaume
> Flandin
> > > > <[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>
> > > > <mailto:[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>>
> > > > > > <mailto:[log in to unmask]
> <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>
> > > > <mailto:[log in to unmask]
> <mailto:[log in to unmask]> <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>
> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>
> <mailto:[log in to unmask] <mailto:[log in to unmask]>>>>>>> wrote:
> > > > > >
> > > > > > Dear Alina,
> > > > > >
> > > > > > How did you extract the data for a
> given voxel?
> > > What is
> > > > > displayed if,
> > > > > > when looking at results, you move the
> 'current
> > > voxel' (red
> > > > > arrow) to
> > > > > > your voxel of interest and do a right
> click
> > while
> > > on the
> > > > glass
> > > > > brain and
> > > > > > select Extract data > betas > this
> voxel in the
> > > contextual
> > > > > menu that
> > > > > > opens?
> > > > > >
> > > > > > Best regards,
> > > > > > Guillaume.
> > > > > >
> > > > > >
> > > > > > On 03/04/17 12:51, Alina Dinu wrote:
> > > > > > > Dear all,
> > > > > > >
> > > > > > > I am interested in the beta values
> for certain
> > > activated
> > > > > voxels.I
> > > > > > extracted them from the beta_0001
> file. I have a
> > > couple of
> > > > > questions:
> > > > > > > 1. Could someone please tell me if
> this is
> > this the
> > > > correct
> > > > > file?
> > > > > > (given that I have a block design with
> only one
> > > condition)
> > > > > > > 2. After I plot them I notice that
> the values
> > > are too high
> > > > > (in the
> > > > > > order of 80-100) which is nonsensical
> for beta
> > > values. Could
> > > > > someone
> > > > > > please tell me if there is any kind of
> scalling
> > > done in
> > > > this file?
> > > > > > How are these values coded?
> > > > > > > 3. Could someone please tell me if this
> > file also
> > > > includes the
> > > > > > confound mean predictor?
> > > > > > >
> > > > > > > Kind regards,
> > > > > > > Alina
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > Guillaume Flandin, PhD
> > > > > > Wellcome Trust Centre for Neuroimaging
> > > > > > University College London
> > > > > > 12 Queen Square
> > > > > > London WC1N 3BG
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > Guillaume Flandin, PhD
> > > > > Wellcome Trust Centre for Neuroimaging
> > > > > University College London
> > > > > 12 Queen Square
> > > > > London WC1N 3BG
> > > > >
> > > > >
> > > >
> > > > --
> > > > Guillaume Flandin, PhD
> > > > Wellcome Trust Centre for Neuroimaging
> > > > University College London
> > > > 12 Queen Square
> > > > London WC1N 3BG
> > > >
> > > >
> > >
> > > --
> > > Guillaume Flandin, PhD
> > > Wellcome Trust Centre for Neuroimaging
> > > University College London
> > > 12 Queen Square
> > > London WC1N 3BG
> > >
> >
> > --
> > Guillaume Flandin, PhD
> > Wellcome Trust Centre for Neuroimaging
> > University College London
> > 12 Queen Square
> > London WC1N 3BG
> >
> >
>
> --
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG
>
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
|