combine orthogonal stacks

[Dianne Patterson]

Dear Experts,

I don't know if this is even possible, but I'm hoping you can help. I have
3 clinical T1 scans in NIFTI format:
one has good resolution in the axial plane
one has good resolution in the coronal plane
one has good resolution in the sagittal plane

My dream is to combine the 3 orthogonal planes into a single
high-resolution 3d image.
Is such a thing possible? Does anyone have suggestions?

Thanks so much,

Dianne


--
Dianne Patterson, Ph.D.
Research Scientist
[hidden email] <[hidden email]>
or
[hidden email]
University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
==============
If you don't hear back from me (and you expected to),
I blame the University's new SPAM filter.
Please write to my gmail account.
==============
Antipiphany: That moment when you realize how little you actually know
==============

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Albert Cardona-2]

Dear Diane,

It should be possible. Would need more details on the volumes, such as x,y,z resolution of each view, and whether the 3 views are already registered or need to be registered. Could you make a sample public?

And may I suggest you bring this question to the forum, where many more eyes will see it? It's at https://forum.image.sc/

Best,

Albert

> On Mar 2, 2019, at 3:31 PM, Dianne Patterson <[hidden email]> wrote:
>
> Dear Experts,
>
> I don't know if this is even possible, but I'm hoping you can help. I have
> 3 clinical T1 scans in NIFTI format:
> one has good resolution in the axial plane
> one has good resolution in the coronal plane
> one has good resolution in the sagittal plane
>
> My dream is to combine the 3 orthogonal planes into a single
> high-resolution 3d image.
> Is such a thing possible? Does anyone have suggestions?
>
> Thanks so much,
>
> Dianne
>
>
> --
> Dianne Patterson, Ph.D.
> Research Scientist
> [hidden email] <[hidden email]>
> or
> [hidden email]
> University of Arizona
> Speech and Hearing Science 314
> 1131 E 2nd Street, Building #71
> (Just East of Harvill)
> ==============
> If you don't hear back from me (and you expected to),
> I blame the University's new SPAM filter.
> Please write to my gmail account.
> ==============
> Antipiphany: That moment when you realize how little you actually know
> ==============
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Robert Dougherty]

On Mar 3, 2019, at 11:29 AM, Robert Dougherty <[hidden email]> wrote:

Diane and Albert,

That seems like an interesting mathematical problem of how to combine the three scans after the rotation and registration issues are handled. I’m pretty sure the average would not give the best resolution. It would combine the blurs from all three scans. There is a case to made for the median, but I suspect the minimum is the first method to try. The logic would be to imagine that blurring is an error that can only increase the value at a voxel. The scan with the lowest value for a given voxel is therefore the most accurate.
The values of three scans obviously have to to scaled correctly relative to each other for this to work as expected. Suppose there is one bright point thing.  Then we want the scans to be scaled so that all three show the highest point at the same brightness, even if the amount of blurring is different.

Bob

> On Mar 2, 2019, at 6:25 PM, Albert Cardona <[hidden email] <mailto:[hidden email]>> wrote:
>
> Dear Diane,
>
> It should be possible. Would need more details on the volumes, such as x,y,z resolution of each view, and whether the 3 views are already registered or need to be registered. Could you make a sample public?
>
> And may I suggest you bring this question to the forum, where many more eyes will see it? It's at https://forum.image.sc/ <https://forum.image.sc/>
>
> Best,
>
> Albert
>
>
>> On Mar 2, 2019, at 3:31 PM, Dianne Patterson <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> Dear Experts,
>>
>> I don't know if this is even possible, but I'm hoping you can help. I have
>> 3 clinical T1 scans in NIFTI format:
>> one has good resolution in the axial plane
>> one has good resolution in the coronal plane
>> one has good resolution in the sagittal plane
>>
>> My dream is to combine the 3 orthogonal planes into a single
>> high-resolution 3d image.
>> Is such a thing possible? Does anyone have suggestions?
>>
>> Thanks so much,
>>
>> Dianne
>>
>>
>> --
>> Dianne Patterson, Ph.D.
>> Research Scientist
>> [hidden email] <mailto:[hidden email]> <[hidden email] <mailto:[hidden email]>>
>> or
>> [hidden email] <mailto:[hidden email]>
>> University of Arizona
>> Speech and Hearing Science 314
>> 1131 E 2nd Street, Building #71
>> (Just East of Harvill)
>> ==============
>> If you don't hear back from me (and you expected to),
>> I blame the University's new SPAM filter.
>> Please write to my gmail account.
>> ==============
>> Antipiphany: That moment when you realize how little you actually know
>> ==============
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

Robert P. Dougherty
President
OptiNav, Inc.
1414 127th Pl NE #106
Bellevue, WA 98005
[phone]
FAX [phone]
[hidden email] <mailto:[hidden email]>
www.optinav. com


Robert P. Dougherty
President
OptiNav, Inc.
1414 127th Pl NE #106
Bellevue, WA 98005
[phone]
FAX [phone]
[hidden email]
www.optinav. com


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mario Emmenlauer-3]

Dear Diane and all,

the problem sounds similar to what can be found in the SPIM
microscope setting, see https://imagej.net/SPIM_Registration. In
this case, the Richardson–Lucy deconvolution was successfully
applied to find the (higher resolution) original image that
would contribute to the (lower resolution) individual views.

See for example https://en.wikipedia.org/wiki/Richardson%E2%80%93Lucy_deconvolution

It may be at least interesting to see if something like the
SPIM plugin could help, and Stephan Preibisch is usually quite
responsive.

All the best,

     Mario



On 03.03.19 20:40, Robert Dougherty wrote:

> On Mar 3, 2019, at 11:29 AM, Robert Dougherty <[hidden email]> wrote:
>
> Diane and Albert,
>
> That seems like an interesting mathematical problem of how to combine the three scans after the rotation and registration issues are handled. I’m pretty sure the average would not give the best resolution. It would combine the blurs from all three scans. There is a case to made for the median, but I suspect the minimum is the first method to try. The logic would be to imagine that blurring is an error that can only increase the value at a voxel. The scan with the lowest value for a given voxel is therefore the most accurate.
> The values of three scans obviously have to to scaled correctly relative to each other for this to work as expected. Suppose there is one bright point thing.  Then we want the scans to be scaled so that all three show the highest point at the same brightness, even if the amount of blurring is different.
>
> Bob
>
>
>> On Mar 2, 2019, at 6:25 PM, Albert Cardona <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> Dear Diane,
>>
>> It should be possible. Would need more details on the volumes, such as x,y,z resolution of each view, and whether the 3 views are already registered or need to be registered. Could you make a sample public?
>>
>> And may I suggest you bring this question to the forum, where many more eyes will see it? It's at https://forum.image.sc/ <https://forum.image.sc/>
>>
>> Best,
>>
>> Albert
>>
>>
>>> On Mar 2, 2019, at 3:31 PM, Dianne Patterson <[hidden email] <mailto:[hidden email]>> wrote:
>>>
>>> Dear Experts,
>>>
>>> I don't know if this is even possible, but I'm hoping you can help. I have
>>> 3 clinical T1 scans in NIFTI format:
>>> one has good resolution in the axial plane
>>> one has good resolution in the coronal plane
>>> one has good resolution in the sagittal plane
>>>
>>> My dream is to combine the 3 orthogonal planes into a single
>>> high-resolution 3d image.
>>> Is such a thing possible? Does anyone have suggestions?
>>>
>>> Thanks so much,
>>>
>>> Dianne
>>>
>>>
>>> --
>>> Dianne Patterson, Ph.D.
>>> Research Scientist
>>> [hidden email] <mailto:[hidden email]> <[hidden email] <mailto:[hidden email]>>
>>> or
>>> [hidden email] <mailto:[hidden email]>
>>> University of Arizona
>>> Speech and Hearing Science 314
>>> 1131 E 2nd Street, Building #71
>>> (Just East of Harvill)
>>> ==============
>>> If you don't hear back from me (and you expected to),
>>> I blame the University's new SPAM filter.
>>> Please write to my gmail account.
>>> ==============
>>> Antipiphany: That moment when you realize how little you actually know
>>> ==============
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>
> Robert P. Dougherty
> President
> OptiNav, Inc.
> 1414 127th Pl NE #106
> Bellevue, WA 98005
> [phone]
> FAX [phone]
> [hidden email] <mailto:[hidden email]>
> www.optinav. com
>
>
> Robert P. Dougherty
> President
> OptiNav, Inc.
> 1414 127th Pl NE #106
> Bellevue, WA 98005
> [phone]
> FAX [phone]
> [hidden email]
> www.optinav. com
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

Viele Gruesse,

     Mario Emmenlauer


--
BioDataAnalysis GmbH, Mario Emmenlauer      Tel. Buero: [phone]
Balanstr. 43                   mailto: memmenlauer * biodataanalysis.de
D-81669 München                          http://www.biodataanalysis.de/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html