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

[Dorian P.]

I have been able finally to back project the ROIs for a single fasciculus
and export them one by one. If you have an automatic TRS creation code (IDL
or executables) that would make things much easier. I can maybe do as
Yajing suggest, backproject the WMPM, but how to create the roi sets again
without doing it one by one manually? This is something hopefully to do
routinely for patients.

Thank you all.

Dorian

2013/1/31 Yajing Zhang <zhangyajing9996 at gmail.com>

> Hi,
>
> I used IDL code for batch processing, and I think our executable functions
> can do the same thing. Because TRS is a set of labels of ROI in the WMPM
> type II, back-projection of TRS is corresponding to back-projection of the
> atlas parcellation map using Hmap (provided by LDDMM).
>
> As for the ROI display, the intensity value is "1", so you can adjust the
> visualization scale as suggested below.
>
>
> Yajing
>
>
> On Thu, Jan 31, 2013 at 2:37 PM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> 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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