Although some images (e.g. DTI, PET) are more sensitive to the changes in the acquisition parameters. But this is applicable to all imaging data. e.g. if you have T1 images acquired with different acquisition parameters then this will affect the size of the matrix, and the slices thickness. As a result, you will not be able at the end of the analysis to differentiate if the differences between the study groups are related to a pathology, or it is because of  the difference in acquisition parameters.

The reason why I am looking for a method to normalize the images acquired using different acquisition parameters to include them in the same pipeline.




Hi Stephen,

I have been reading the link. Is this applicable to MRI data or just only for DTI data?...and..why?

Yours sincerely,

Rosalia

2016-09-03 12:56 GMT+02:00 Stephen Smith <[log in to unmask]>:
Hi - see the FAQ entry:
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/Faq

Cheers.




On 3 Sep 2016, at 11:52, Antoine Nasimian <[log in to unmask]> wrote:

Hi Steve,
I highly appreciate your response.
I have DTI data aquired using different aquisition parameters ( same b value, but different TE and TR).

I was thinking of kind of normalization for the images permits of including it, regardless the differences in TE, TR in the same analysis (e.g TBSS)
I know aquision parameters like TE can affect FA value. How can I include different FA maps (i.e FA maps generated from DWI aquired using different aquisition parameters) in the same TBSS analysis.
Can intensity normalization be of benifits in here?

Best,
Ant



Hi

On 2 Sep 2016, at 12:18, Jon Anderson <[log in to unmask]> wrote:

Dear FSL experts,
I would like to ask the following questions about " intensity normalization in FSL":

1. In which circumstances, intensity normalization (i.e. the flag -inm in the command " fslmaths") is urgent?

I'm not sure what you're asking here, sorry - but maybe the below answer gives you what you need.

2. What type of images can be normalized? Are there any benefits of intensity normalization in DTI data?

In general this is NOT done for inputs to TBSS, as the various dtifit outputs (eg FA, MD) are supposed to already be directly comparable across subjects as long as all subjects were acquired in the same way.

Cheers.


3. Can I use the flag "-inm "in the command "fslmaths" in the script "tbss_3_postreg" to normalize the images "all_FA" then continue with the rest of the pipeline? I am wondering if the image "all_FA" is 2D or 3D?

Thanks for any comment and for your help!

Jon




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Rosalía Dacosta-Aguayo, Post-Doctoral Researcher.
Biomedicine, PhD
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Gaixotasun Neuroendekapenezko Taldea
Neurozientziak Arloa

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