# FA from volume- how to do it

**URL:** <https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123>\
**Category:** Support\
**Created:** [December 18, 2018, 12:37pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123 "2018-12-18T12:37:37Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![Ania](https://avatars.discourse-cdn.com/v4/letter/a/58f4c7/32.png) [@Ania](https://discourse.slicer.org/u/Ania)\
**Post date:** [December 18, 2018, 12:37pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/1 "2018-12-18T12:37:37Z")

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Dear all,

I am completely new to 3dSlicer, and I’m wondering: Is it possible to estimate FA from concrete ROI/Volume?  
I’ve got nii Fractional Anisotropy maps as input. I am able to draw a volume, but I’ve got no idea what’s next.

I would be grateful for any advice.

Ania

Operating system:  
Slicer version:  
Expected behavior:  
Actual behavior:

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [December 18, 2018, 6:53pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/2 "2018-12-18T18:53:35Z")

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Hi - it sounds like you just need the Segment Editor and Segment Statistics modules.

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**Author:** ![Ania](https://avatars.discourse-cdn.com/v4/letter/a/58f4c7/32.png) [@Ania](https://discourse.slicer.org/u/Ania)\
**Post date:** [December 19, 2018, 11:41am UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/3 "2018-12-19T11:41:58Z")

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Thank you for you reply, Steve.

The problem is, that as I see, with Segment Statistic module I can not obtain Fractional Anisotropy or mean diffusivity.  
I tried to use the Diffusion Tensor Scalar Maps segment ( as I can see you can estimate both FA and MD here), but it always says: " No input data assigned to Input DTI Volume" . I try to assign the input but I dont really know how.

Ania

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**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [December 19, 2018, 12:43pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/4 "2018-12-19T12:43:57Z")

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> [@Ania](#):
>
> I’ve got nii Fractional Anisotropy maps as input.

> [@Ania](#):
>
> I tried to use the Diffusion Tensor Scalar Maps segment ( as I can see you can estimate both FA and MD here)

If you already have an FA map calculated in nifti, as in the first quote, then those maps can be used directly as input to the statistics – no need to use the Scalar Maps module.

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**Author:** ![Ania](https://avatars.discourse-cdn.com/v4/letter/a/58f4c7/32.png) [@Ania](https://discourse.slicer.org/u/Ania)\
**Post date:** [December 19, 2018, 1:14pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/5 "2018-12-19T13:14:41Z")

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Thank you Isaiah, I tried to do this, but after I create a volume on this FA maps I cannot choose it as an input…

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**Author:** ![Ania](https://avatars.discourse-cdn.com/v4/letter/a/58f4c7/32.png) [@Ania](https://discourse.slicer.org/u/Ania)\
**Post date:** [December 20, 2018, 3:14pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/6 "2018-12-20T15:14:05Z")

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![Bez%C2%A0tytu%C5%82u](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/6/06c20ec02aa13f637e5e630caade6dd27699965a.jpeg)

I manage to create that table but I am not sure if the ‘minimum, maximum, mean’ relates to FA.  
Of course it is based on FA maps, from which I created a segmentation which I took as an input.

Ania

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**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [December 20, 2018, 3:17pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/7 "2018-12-20T15:17:03Z")

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> [@Ania](#):
>
> I am not sure if the ‘minimum, maximum, mean’ relates to FA.

Those statistics are calculated for all of the voxels in the selected segment.

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**Author:** ![Ania](https://avatars.discourse-cdn.com/v4/letter/a/58f4c7/32.png) [@Ania](https://discourse.slicer.org/u/Ania)\
**Post date:** [December 20, 2018, 3:21pm UTC](https://discourse.slicer.org/t/fa-from-volume-how-to-do-it/5123/8 "2018-12-20T15:21:27Z")

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Okay, that’s good. Thank you! But still I don’t know what’s the maximum and minimum (max and min FA or not really?)