Hi,
It depends what intensities are in your image.
If you look at it in the normal mode (not the 3D viewer) and
pick some "standard" voxels - what is their intensity?
This is what you need to use to guide your choice.
Anything below what you choose will disappear in the 3D view.
All the best,
Mark
On 19 Oct 2009, at 17:10, Jeremy Young wrote:
> 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
>>>>
>>>>
>>>
>>
>>
>
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