Hello,

Sorry for being unable to understand this better, but how do you find  
a sensible value for an intensity image? I tried playing with numbers  
between 0 and 100000, concentrating around 5500 area especially, but  
to no avail.

Thanks,
Jeremy


On Oct 16, 2009, at 10:55 AM, Mark Jenkinson wrote:

> Hi,
>
> It is not min and max that you need to change.
> These are display ranges for the intensity image, not
> the threshold applied to create the 3D image.  The
> box you need to change is the one to the right of
> the surface and camera buttons: that is, number 5 in
>   http://www.fmrib.ox.ac.uk/fsl/fslview/3D-vtkkbd.html
>
> If you set this to a sensible value based on your
> intensity image, then hopefully it will give you a good result.
>
> All the best,
> 	Mark
>
> On 16 Oct 2009, at 15:30, Jeremy Young wrote:
>
>> Thanks guys.
>>
>> It seems like though that when I load 3D viewer my minimum is set  
>> at 0. Playing with the Min and Max does not seem to help.
>>
>> I am looking at a subject's brain extracted brain in T1 and a  
>> normalized and thresholded probtrackx path, tracked in T1 space if  
>> that helps any.
>>
>> Jeremy
>>
>>
>> On Oct 15, 2009, at 3:15 PM, Dave Flitney wrote:
>>
>>> Yes. The "No data to decimate" message means your threshold value  
>>> is too high.
>>>
>>> ------Original Message------
>>> From: Mark Jenkinson
>>> Sender: FSL - FMRIB's Software Library
>>> To: [log in to unmask]
>>> ReplyTo: FSL - FMRIB's Software Library
>>> Subject: Re: [FSL] fslview 3D viewer error
>>> Sent: 15 Oct 2009 19:27
>>>
>>> Hi,
>>>
>>> This might just be to do with an appropriate threshold.
>>> Check your intensities and make sure that the value
>>> in the box to the right of the surface and camera
>>> buttons is set to a value that is not too high.
>>>
>>> All the best,
>>> 	Mark
>>>
>>>
>>> On 15 Oct 2009, at 19:10, Jeremy Young wrote:
>>>
>>>> Hi,
>>>>
>>>> When I try to run the 3D viewer in fslview I get the following
>>>> errors in the terminal window and nothings loads where the 3D
>>>> structure is supposed to be:
>>>> ERROR: In /var/tmp/bach-build/BUILD/VTK/Graphics/ 
>>>> vtkDecimatePro.cxx,
>>>> line 161
>>>> vtkDecimatePro (0x14432ef0): No data to decimate!
>>>>
>>>> ERROR: In
>>>> /var/tmp/bach-build/BUILD/VTK/Graphics/vtkSmoothPolyDataFilter.cxx,
>>>> line
>>>> 212
>>>> vtkSmoothPolyDataFilter (0x143b2b70): No data to smooth!
>>>>
>>>> ERROR: In /var/tmp/bach-build/BUILD/VTK/Graphics/
>>>> vtkPolyDataNormals.cxx,
>>>> line 94vtkPolyDataNormals (0x143b3360): No data to generate normals
>>>> for!
>>>>
>>>> Would this have anything to do with the computer's recent  
>>>> upgrade to
>>>> the latest CentOS? I haven't used the 3D viewer in a very long time
>>>> though.
>>>>
>>>> Cheers,
>>>> Jeremy
>>>>
>>>
>>>
>>>
>>> Sent using BlackBerry® from Orange
>>>
>>>
>>
>
>