Sorry for this. My suggestion:
> mycmap = colormap([gray(64); nan nan nan ;jet(63)]);
>
does not do the right thing. The solution is to put NaN in the image on
the places where the value is not to be plotted.
best
Torben
> 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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