[Mristudio-users] ICBM_DTI_81 image registration

[Shaimaa Abdelsattar]

Hello experts,
I've got confused. Please revise with me the steps i followed to find where was the mistake.
1.First i uploaded my philips dicom data and transformed it to rec files.
2. Then i applied AIR in Dti studio using affine transformation, then I save the resulting image as .rec file again
3. I performed tensor calculations in dti mapping, and i saved FA file.
4. I coregistered fa with ICBM_DTI_81 FA map in diffeomap again choosing affine. 
5. I opened the updated fa in Roi editor and then i opened wmpm 90%
6. I found some rois  were perfectly matched and others were larger than the anatomical areas

My images were 144* 144
And fov were 230 * 230
Slice thickness 2
Image blocks 1
Nex 1
Image slices 70

Please tell my how can i adjust the roi file over my anatomical areas

Sorry for taking your time and thank you for your concern

Thanks
Shaimaa


On Nov 15, 2013, at 5:42 PM, "Hangyi Jiang" <hjiang at jhmi.edu> wrote:

> 
> we usually do AIR before Deffiomap, not after,
> 
> hangyi
> 
> 
> From: Shaimaa Abdelsattar [shaimaa96 at hotmail.com]
> Sent: Friday, November 15, 2013 10:46 AM
> To: Hangyi Jiang
> Subject: Re: [Mristudio-users] ICBM_DTI_81 image registration
> 
> So after i do registration in deffiomap program, i should perform Air in dti studio 
> My question was about  image registration using ICBM_DTI_81 atlas
> 
>>>>> I have question about image registration. I have used ICBM_DTI_81 atlas for image registration in my case, control clinical research using linear transformation. After doing this i found good registration after i tested structures by the landmark option. Yet when i applied their  ROI file (WMPM 90%) on my data, I found that the ROIs  in the atlas are larger  than the actual size of structures of my patients. Is there any solution for this?
> 
> 
> On Nov 15, 2013, at 5:34 PM, "Hangyi Jiang" <hjiang at jhmi.edu> wrote:
> 
>> 
>> when you do AIR using DtiStudio. the AIR parameter dialog shows two options:
>> 
>> Rigid Body, this is a 6 parameters transformation method. (or 6 mode as some one said, not strictly);
>> Affine, this is 12 parameters method (or 12 mode..)
>> 
>> there is no separate 9 mode selection. it is already included in 12 mode.
>> 
>> hangyi
>>  
>> 
>> 
>> From: Shaimaa Abdelsattar [shaimaa96 at hotmail.com]
>> Sent: Friday, November 15, 2013 10:33 AM
>> To: Hangyi Jiang
>> Subject: Re: [Mristudio-users] ICBM_DTI_81 image registration
>> 
>> Thank you,
>> Where can i find the option to choose 9 or 12 mode to adjust my transformation
>> 
>> Thanks again
>> 
>> On Nov 15, 2013, at 3:41 PM, "Hangyi Jiang" <hjiang at jhmi.edu> wrote:
>> 
>>> 
>>> affine transformation includes scaling.
>>> 
>>> hangyi
>>> 
>>> 
>>> 
>>> From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] on behalf of Shaimaa Abdelsattar [shaimaa96 at hotmail.com]
>>> Sent: Friday, November 15, 2013 5:03 AM
>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>>> Subject: Re: [Mristudio-users] ICBM_DTI_81 image registration
>>> 
>>> Hello Dr.Mori, 
>>> I tried affine transformation and trilinear interpolation
>>> How can i include scaling in my linear transformation ? 
>>> 
>>> Thanks
>>> 
>>> 
>>> On Nov 14, 2013, at 4:10 PM, "Susumu Mori" <smoriw at gmail.com> wrote:
>>> 
>>>> Hi Shaimaa,
>>>> 
>>>> When you apply the linear registration, did you use 9 or 12-mode, which includes scaling?
>>>> ICBM-152 template brain is larger than many subjects. So, your linear transformation better include scaling. 
>>>> 
>>>> Usually the parcellation map superimpose pretty well.
>>>> 
>>>> 
>>>> On Wed, Nov 13, 2013 at 2:38 PM, Shaimaa Abdelsattar <shaimaa96 at hotmail.com> wrote:
>>>>> Hi experts,
>>>>> I have question about image registration. I have used ICBM_DTI_81 atlas for image registration in my case, control clinical research using linear transformation. After doing this i found good registration after i tested structures by the landmark option. Yet when i applied their  ROI file (WMPM 90%) on my data, I found that the ROIs  in the atlas are larger  than the actual size of structures of my patients. Is there any solution for this?
>>>>> 
>>>>> Or i should use other atlas for my registration
>>>>> 
>>>>> Thanks
>>>>> Shaimaa
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