[Mristudio-users] Backprojecting template roi sets (TRS)

[Dorian P.]

Yes, I have managed to see the rois by adjusting the view, but still can't
do the back projection. The manual matrix transformation
(Hmap->InvertedAIR) gives the result in  181x217x181 instead of my
128x128x66. See attached.

Thank you.

[image: Immagine in linea 1]
2013/1/31 susumu mori <susumu at mri.jhu.edu>

> Hi Dorian,
>
> I think it is just a matter of display intensity. The ROI locations have
> "1" and non-ROI pixels are "0". So, you have to right click on the image
> (looks like blank) and adjust the display intensity scale to see the dark
> ROIs (1 out of 256 grayscale is not visible).
>
> As for the batch processing of TRS to each subject data, we have
> executable codes.
> Xin and Hangyi, maybe we should post the executables somewhere in
> www.mristudio.org?
>
> Yajing, how did you apply the TRS to each subject? Did you use IDL codes
> and the executables or did you use MriStudio one-by-one?
>
> On Thu, Jan 31, 2013 at 12:46 PM, Dorian P. <alb.net at gmail.com> wrote:
>
>> Hi,
>>
>> Just wanted to renovate this question. It is not clear to me how to
>> backproject TRS files, or whether I should do it for the whole WMPM type II
>> atlas.
>>
>> The only way I could make atlas fiber tracking now is by projecting
>> tensors in normalized and by manually creating a .map file for rois of a
>> fasciculus. The TRS that are for download don't work in DTIstudio.
>>
>> Thank you.
>>
>> Dorian
>>
>> 2013/1/30 Dorian P. <alb.net at gmail.com>
>>
>> Hi all,
>>>
>>> I am trying to do atlas based tract reconstruction based on Zhang Yajing
>>> (2010) paper. I have performed LDDMM and need to backproject a Template Roi
>>> Set (say the uncinate). The files in the TRS look like this:
>>>
>>> ROI_display.roihdr
>>> AND_#1.dat
>>> NOT.dat
>>> OR.dat
>>> ROI_display.dat
>>>
>>> I tried loading the these files in Diffeomap but there are no white
>>> pixels, all black. So, how ca I do this back projection?
>>>
>>>
>>> And is there an automatic way to massively invert TRS's in native space
>>> or do I have to go one by one for each TRS to open and save in Diffeomap.
>>>
>>>
>>>  Thank you.
>>>
>>
>>
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>
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