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

[Bharti Rana]

Hi

I think Co-registration of your FA map, T1 image with automated
parcellation atlas may resolve your problem.


On Mon, Aug 12, 2013 at 11:07 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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Best Regards
Bharti
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