[Mristudio-users] fiber tracking

Tue Jan 12 13:59:28 EST 2010

It's hard to tell. Usually, it is often difficult to reconstruct the entire
CST all the way from the medulla to the motor cortex because it's very long
and also penetrate regions with complex fiber structures such as the pons.

On Tue, Jan 12, 2010 at 11:20 AM, Sona Saksena <saksena.sona at gmail.com>wrote:

> Hello,
>
> Thanks for the reply. I am facing a problem regarding the reconstruction of
> fibre tracts. I want to track the CST fibres of a tumor patient, after
> placing the ROI on the CST at the level of medulla the tracts are generated
> but they are not exactly the same as shown in publications (reconstructed
> fibers are not fine and refined).
>
> I have taken the following fiber tracking parameters:
>
> Start Tracking
> if FA>0.25
>
> Stop Tracking
> if FA<0.25
> if Tract turning-angle>45
>
> Flip Eigen Vector
>
> X, Y, Z components have been checked
>
> I am attaching a print screen shot of the image, please suggest some
> changes.
> regards
>
> sona
> On Mon, Jan 11, 2010 at 11:56 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> The statistics in the ROI panel is to measure pixel values inside the ROI.
>> It is just a simple ROI-based quantification.
>>
>> In the fiber panel, you draw ROI to create tract paths. Then the
>> quantification is based on pixel values of the reconstructed fibers.
>>
>>
>> On Fri, Jan 8, 2010 at 3:47 PM, Sona Saksena <saksena.sona at gmail.com>wrote:
>>
>>> Hello,
>>>
>>> After placing the ROI, the statistics for the mostly recent ROI is shown
>>> in the fiber control panel. What is the difference between the statistics
>>> after pressing the "Go button" in the "Fiber Statistics" option and the most
>>> recent statisitcs in the ROI control panel. What should I take for my final
>>> calculations and results.
>>>
>>> Please do suggest.
>>>
>>> thanks
>>>
>>> regards
>>>
>>> sona
>>>
>>>   On Fri, Jan 8, 2010 at 12:53 PM, susumu mori <susumu at mri.jhu.edu>wrote:
>>>
>>>> Hi Sona,
>>>>
>>>> There is detailed description about the "flip" function in the manual.
>>>> the truth is, nobody is sure about the sign because scanners can change it
>>>> dynamically depending on your scan protocol.
>>>> There is a way to rigorously solve this problem, but it is very
>>>> difficult and that's why we just empirically solve it by checking all 4
>>>> options (no check, x, y, z flipped). Good news is, if the signs are wrong,
>>>> tracking doesn't make sense.
>>>>
>>>>
>>>> On Fri, Jan 8, 2010 at 10:34 AM, Sona Saksena <saksena.sona at gmail.com>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Thanks for your suggestion. There is a option in the fiber tracking
>>>>> parameters "Flip Eigen Vector". Do I have to use this check box?
>>>>>
>>>>> Actually we have applied gradients in 26 directions (GE
>>>>> Scanner, 3Tesla). I am not sure about the sign of all of the components in
>>>>> the gradient table.  What shall I do?
>>>>>
>>>>> This is the gradient table.
>>>>>
>>>>>
>>>>> 0: 0.000000, 0.000000, 0.000000
>>>>>
>>>>> 1: 1.000000, 0.000000, 0.000000
>>>>>
>>>>> 2: 0.849000, 0.528000, 0.000000
>>>>>
>>>>> 3: -0.108000, 0.565000, 0.818000
>>>>>
>>>>> 4: 0.884000, -0.345000, -0.315000
>>>>>
>>>>> 5: -0.003000, -0.736000, 0.677000
>>>>>
>>>>> 6: -0.868000, -0.238000, 0.436000
>>>>>
>>>>> 7: 0.799000, 0.370000, 0.475000
>>>>>
>>>>> 8: -0.162000, 0.987000, 0.000000
>>>>>
>>>>> 9: 0.866000, -0.129000, 0.483000
>>>>>
>>>>> 10: -0.212000, -0.936000, 0.281000
>>>>>
>>>>> 11: 0.068000, -0.892000, -0.446000
>>>>>
>>>>> 12: 0.550000, -0.544000, -0.634000
>>>>>
>>>>> 13: -0.435000, -0.422000, 0.795000
>>>>>
>>>>> 14: -0.599000, 0.780000, 0.182000
>>>>>
>>>>> 15: -0.525000, 0.030000, -0.851000
>>>>>
>>>>> 16: -0.600000, -0.688000, 0.409000
>>>>>
>>>>> 17: 0.653000, -0.060000, -0.755000
>>>>>
>>>>> 18: 0.207000, -0.076000, -0.975000
>>>>>
>>>>> 19: -0.413000, -0.699000, -0.584000
>>>>>
>>>>> 20: -0.436000, 0.822000, -0.366000
>>>>>
>>>>> 21: 0.462000, 0.874000, 0.148000
>>>>>
>>>>> 22: -0.503000, 0.488000, -0.713000
>>>>>
>>>>> 23: 0.824000, -0.530000, 0.202000
>>>>>
>>>>> 24: 0.297000, 0.349000, 0.889000
>>>>>
>>>>> 25: -0.040000, 0.318000, -0.947000
>>>>>
>>>>>
>>>>>
>>>>> Please do suggest?
>>>>>
>>>>>
>>>>>
>>>>> regards
>>>>>
>>>>>
>>>>>
>>>>> sona
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>   On Thu, Jan 7, 2010 at 3:32 PM, susumu mori <susumu at mri.jhu.edu>wrote:
>>>>>
>>>>>> Hi Sona,
>>>>>>
>>>>>> I suggest you to go through the manual section in www.mristudio.org.
>>>>>> There you can find a user's manual for DtiStudio. It gives you the
>>>>>> step-by-step procedure for tensor calculation and fiber tracking.
>>>>>>
>>>>>>   On Thu, Jan 7, 2010 at 2:48 PM, Sona Saksena <
>>>>>> saksena.sona at gmail.com> wrote:
>>>>>>
>>>>>>>   Hello,
>>>>>>>
>>>>>>> Please can you tell me steps of performing fiber tracking in brain
>>>>>>> tumor patients using DTI studio. The DTI data is on 3T GE scanner with
>>>>>>> gradients applied in 26 directions. How to generate the reconstructed
>>>>>>> fibres?
>>>>>>>
>>>>>>> thanks
>>>>>>>
>>>>>>> regards
>>>>>>>
>>>>>>> Sona Saksena
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Mristudio-users mailing list
>>>>>>> Mristudio-users at mristudio.org
>>>>>>> http://lists.mristudio.org/mailman/listinfo/
>>>>>>> Unsubscribe, send a blank email to:
>>>>>>> Mristudio-users-unsubscribe at mristudio.org
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mristudio-users mailing list
>>>>>> Mristudio-users at mristudio.org
>>>>>> http://lists.mristudio.org/mailman/listinfo/
>>>>>> Unsubscribe, send a blank email to:
>>>>>> Mristudio-users-unsubscribe at mristudio.org
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Sona Saksena
>>>>> Ph. D Scholar
>>>>>
>>>>> _______________________________________________
>>>>> Mristudio-users mailing list
>>>>> Mristudio-users at mristudio.org
>>>>> http://lists.mristudio.org/mailman/listinfo/
>>>>> Unsubscribe, send a blank email to:
>>>>> Mristudio-users-unsubscribe at mristudio.org
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Mristudio-users mailing list
>>>> Mristudio-users at mristudio.org
>>>> http://lists.mristudio.org/mailman/listinfo/
>>>> Unsubscribe, send a blank email to:
>>>> Mristudio-users-unsubscribe at mristudio.org
>>>>
>>>>
>>>
>>>
>>> --
>>> Sona Saksena
>>> Ph. D Scholar
>>>
>>> _______________________________________________
>>> Mristudio-users mailing list
>>> Mristudio-users at mristudio.org
>>> http://lists.mristudio.org/mailman/listinfo/
>>> Unsubscribe, send a blank email to:
>>> Mristudio-users-unsubscribe at mristudio.org
>>>
>>>
>>
>> _______________________________________________
>> Mristudio-users mailing list
>> Mristudio-users at mristudio.org
>> http://lists.mristudio.org/mailman/listinfo/
>> Unsubscribe, send a blank email to:
>> Mristudio-users-unsubscribe at mristudio.org
>>
>>
>
>
> --
> Sona Saksena
> Ph. D Scholar
>
> _______________________________________________
> Mristudio-users mailing list
> Mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> Mristudio-users-unsubscribe at mristudio.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20100112/dd76b666/attachment.html 