[Mristudio-users] how to apply brain mask for Tensor calculation.

[Susumu Mori]

Hi Ravi,

Our DtiStudio/MriStudio is not really a tool for cross-modal (e.g. T1 vs
DTI) registration, but you can use DiffeoMap to register T1 and DTI images
using AIR built inside DiffeoMap. I believe T1-FA would be difficult
because the contrast is so different and brain boundary is not well
delineated in FA. I would suggest T1-b0 or T1-Sigma(DWI) (=add all DWIs) to
drive the registration. AIR automatically adjust the matrix size and pixel
size.

The registration would not be perfect because T1 and DTI are differently
deformed due to B0 susceptibility.

Alternatively, you can try our direct percellation of DTI data using
DiffeoMap/RoiEditor.

Susumu


On Mon, Aug 12, 2013 at 1:37 AM, Kotikalapudi Raviteja <
raviteja.kotikalapudi at gmail.com> wrote:

> Hi,
>
> I really appreciate your help. I am able to solve the gradient table
> issue. I have co-registered FA maps to their respective T1 images.
> *FA image dimension: 128x128x70*
> *T1 image dimension: 256x256x165*
> *Co-registered image dimensions: 256x256x165*
> *
> *
> *Now, I want to extract FA values for particular ROIs using automated
> parcellation atlas. But for that process to take place, my image dimensions
> should match the dimensions of the parcellation atlas. *
> *
> *
> *Could you please suggest me a way to fix this problem? *
> *Many thanks,*
> *Ravi*
> *
> *
> *
> *
>
>
>
> On Tue, Aug 6, 2013 at 7:06 AM, susumu mori <smoriw at gmail.com> wrote:
>
>> Hi Ravi,
>>
>> are you reading DICOM files?
>> If so, the cause of the crash is usually the DTI image file and the
>> gradient table you specified didn't match.
>> Can you read the file using the "open"  button? If you can read and see
>> the images, count how many 3D volumes are loaded. I believe you can find 34
>> volumes for Philips High table.
>> Then load the same data using DtiMapping, specify the gradient table.
>> Here, make sure you really have 34 rows in the table.
>>
>>
>> On Mon, Aug 5, 2013 at 3:00 AM, Kotikalapudi Raviteja <
>> raviteja.kotikalapudi at gmail.com> wrote:
>>
>>> Dear All,
>>> I am writing in context TENSOR CALCULATION. This is the second project
>>>  for which I am using the DTI Studio. I am using Philips High Angular 32 as
>>> the gradient table.
>>>
>>> *1. While clicking on 'ADC-Map' ,  DTI Studio crashes showing the
>>> following error:*
>>> *     MRI VIEW 3D MFC application has stopped. *
>>> *2. If at all it is successful, Tensor maps which are generated are
>>> wrong.*
>>> *
>>> *
>>> *I feel there is no problem with the computer memory. So do I need to
>>> look into the gradient maps if those were the correct for this research?
>>> *
>>>
>>> Please provide help ASAP. I thank you for your time and consideration.
>>>
>>> Regards,
>>> Ravi
>>>
>>>
>>> On Sun, Aug 4, 2013 at 6:07 AM, susumu mori <smoriw at gmail.com> wrote:
>>>
>>>> Hi YM,
>>>>
>>>> When you do tensor calculation by DtiStudio, after clicking "tensor
>>>> calculation" button, you can set a threshold value to mask out all the
>>>> noise floor outside the brain.
>>>>
>>>>
>>>> On Thu, Aug 1, 2013 at 7:26 AM, Youngmin Huh <ymin1123 at gmail.com>wrote:
>>>>
>>>>> Hi,
>>>>> There is too much noise outside the brain, so I want to apply brain
>>>>> mask to eliminate the noise.
>>>>> I tried to use ROI editor to make brain mask, using skull strip. I
>>>>> obtained mask.nii on scrolldown box and saved it to a dat file.
>>>>> but I could not load it for tensor calculation. I found 'select a
>>>>> mask-image' option, but only subjectname.dat-0, subjectname.dat-1,
>>>>> ...-2, ...-3 was available.
>>>>> how could I apply mask image for Tensor calculation?
>>>>>
>>>>> I would appreciate any comments.
>>>>>
>>>>>
>>>>> YM Huh
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