Let me just add that for avoiding a blue shade across the whole image I
added a couple of nan' s in the colormap:
mycmap = colormap([gray(64); nan nan nan ;jet(63)]);
best
Torben
Torben E. Lund
Danish Research Centre for MR
Copenhagen University Hospital
Kettegaard Allé 30
2650 Hvidovre
Denmark
email: [log in to unmask]
webpage: http://www.drcmr.dk
On 11 Jan 2005, at 15:43, Jan Gläscher wrote:
> Dear Torben,
>
> I guess that you are also hurrying to meet the HBM deadline - so am I.
> So, therefore just a very quick suggestion ...
>
> Check the code of spm_orthviews.m and look for the string
> "addtruecolourimage". There I think you'll find what you want.
>
> Then you want to call spm_orthviews from the command line, because the
> addtruecolourimage option is not bound to the context menu, AFAIK ...
>
> Also, make sure you create a split colormap, by using something like
> this:
>
> mycmap = colormap([gray(64); jet(64)]);
>
> Then you call spm_orthviews like this:
>
> retmap = 'retmap.img'; % or whatever you named it
> mx = 360; % maximum of data range in retmap.img
> mn = 0; % minimum of data range in retmap.img
>
> spm_orthviews('addtruecolourimage',1,retmap,mycmap,0.4,360,0);
>
> Cheers,
> Jan
>
>
>
> On 2005-01-11 (Tue) at 16:07:05 +0100, Torben Ellegaard Lund
> <[log in to unmask]> wrote:
>> Dear Volkmar
>>
>> Thanks for your suggestion I wish it was as simple a that. But in
>> check_reg you can only superimpose an image in different alpha blends
>> of e.g. red this is of little use if you want to correlate an angle to
>> a specific color. What I want is so superimpose an image in say
>> colormap(jet) onto a grayscale image. Much like what one gets in the
>> results section when choosing overlays sections, only I dont have a
>> statistic image rather an image of angles from a retinotopic
>> stimulation. I could of course use FSLview but that is almost too
>> easy!
>>
>> Best Torben
>>
>>
>>
>> Torben E. Lund
>> Danish Research Centre for MR
>> Copenhagen University Hospital
>> Kettegaard Allé 30
>> 2650 Hvidovre
>> Denmark
>> email: [log in to unmask]
>> webpage: http://www.drcmr.dk
>>
>> On 11 Jan 2005, at 15:33, Volkmar Glauche wrote:
>>
>>
>>> On Tue, 11 Jan 2005, Torben Ellegaard Lund wrote:
>>>
>>>
>>>> We have constructed some retinotopic maps and would like to
>>>> superimpose these
>>>> maps (e.g. values from 1 to 360 degrees in say colormap jet) on a
>>>> structural
>>>> image in grayscale. While this is possible on a slice-wise basis
>>>> using
>>>> display_slices, I was wondering how this could be done with
>>>> spm_orth_views?
>>>> Can anybody help?
>>>>
>>>
>>> Try the context menu that comes with each section of an image
>>> displayed
>>> with CheckReg. You can activate this context menu also in other
>>> orthogonal
>>> sections (Display, results overlays etc) by typing
>>>
>>> spm_orthviews addcontext
>>>
>>> at the matlab prompt when image is displayed.
>>>
>>> --
>>> Volkmar Glauche
>>> -
>>> Department of Neurology E-Mail [log in to unmask]
>>> UKE Hamburg Phone 49(0)40-42803-5781
>>> Martinistr. 52 Fax 49(0)40-42803-9955
>>> 20246 Hamburg
>>>
>>
>>
>
> --
> Jan Gläscher Neuroimage Nord
> +49-40-42803-7890 (office) Dept. of Neurology, Bldg S10
> +49-40-42803-9955 (fax) University Hospital
> Hamburg-Eppendorf
> [log in to unmask] Martinistr. 52
> 20246 Hamburg
> Germany
> http://www.uke.uni-hamburg.de/zentren/neuro/neurologie/mitarbeiter/
> glaescher_jan.html
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