There seems a bit trouble to save masked contrast (i.e. choose mask with
others during RESULT). I can get figure and blob in glass brain, as well the
volume, actually everything except a contrast. While the problem now is that
I wanna get a real contrast after masking a negative activation. It would be
convinient to show it in MRIcro, or it may be applied in a third-level analysis.
I find that previously Volkmar got a solution: making an additional mask of the
negative contrast, then applying it in additional design model. It's ok, but is
there a more convinient way to do that now, e.g. in SPM8?
Thanks in advance!
Here I copied that previous lines on this question for your reference:
There is a work-around until the next set of updates:
1) define a contrast you want to use for masking
2) compute results for this contrast (even if it is of no other interest
to you except using it as a mask)
3) compute your target contrast, including the contrast computed above as
On Sat, 31 Mar 2007, Piers Howe wrote:
> Dear Volkmar
> I am having the same problem as Javier. I understand that the bug that
> causes the error message "index exceeds ... error" will be fixed in the
> next update, but in the mean time is there a work-around solution?
> In particular, I get the problem when I try to work through the example in
> the SPM5 manual page 195 "Plotting parametric responses". I get the error
> when I try to use the inclusive mask but apparently the author of the
> manual was able to use the inclusive mask to generate the plot shown in
> Fig 26.17. Why was the author able to suceed whereas I using the same
> program and using the same steps failed?
> Many thanks
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg http://fbi.uniklinik-freiburg.de/
the bug that interactively defined contrasts are not properly saved if
they are not selected for results (which is why you get the "index
exceeds ... error") will be corrected with the next set of updates.
However I do not understand what you would expect to be written out
during masking: Masking is simply an image manipulation operation. It
does not generate any new statistics (effect sizes, extra sum of
squares, T/F values) at voxel level. Thus, the con and T images are
the same as for your unmasked contrast. The only difference is at
cluster level, because the size of your above-threshold clusters may
change due to masking.
Quoting Javier Gonzalez-Castillo <[log in to unmask]>:
> I am working with SPM5 with the last updates. I have analyzed a single
> subject (first level) and defined 5 contrasts for him. I am interested in
> doing some exclusive masking analysis. So I did:
> (1) Press Results
> (2) I selected an existing contrast, let's say contrast1
> (3) Say "Yes" to mask with other contrasts.
> (4) Answer all remaining questions
> Then I get a nice glass brain on the graphics window with the masked data.
> Still nothing gets saved to disk, and I want to have the con files of this
> masked results saved in order to use them as input for a second
> order analysis.
> So I though, let's do the same thing but during the creation of a new
> contrasts. So I did:
> (1) Press Results
> (2) Define a new contrast
> (3) Gave a new name and the contrast definition.
> (3) Press Done in the contrast manager
> (4) Say "Yes" to the question Mask with other contrasts
> (5) Give 0.05 to Uncorrected Mask p-value
> (6) And when I select either Inclusive or Exclusive to the nature of mask,
> the next thing I get is the following error message:
> ??? Index exceeds matrix dimensions.
> Error in ==> spm_getSPM at 397
> str = xCon(Ic).name;
> Error in ==> spm_results_ui at 264
> [SPM,xSPM] = spm_getSPM;
> ??? Error using ==> [hReg,xSPM,SPM] = spm_results_ui;
> Index exceeds matrix dimensions.
> ??? Error while evaluating uicontrol Callback
> My question is why do I get this error? Or how can I do to get the contrast
> files of the masked results, if there is any other way.
> Thanks very much for your help,