# Problem about tensor2metric to generate RD, FA, ADC, MD map

**URL:** https://community.mrtrix.org/t/problem-about-tensor2metric-to-generate-rd-fa-adc-md-map/5066
**Category:** Uncategorized
**Tags:** error
**Created:** [July 20, 2021, 8:46am UTC](https://community.mrtrix.org/t/problem-about-tensor2metric-to-generate-rd-fa-adc-md-map/5066 "2021-07-20T08:46:50Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![CarlisleYun79](https://community.mrtrix.org/user_avatar/community.mrtrix.org/carlisleyun79/32/3410_2.png) [@CarlisleYun79](https://community.mrtrix.org/u/CarlisleYun79)
#### Post date: [July 20, 2021, 8:46am UTC](https://community.mrtrix.org/t/problem-about-tensor2metric-to-generate-rd-fa-adc-md-map/5066/1 "2021-07-20T08:46:51Z")

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Dear experts,

Now I’m using tensor2metric for making the FA, ADC, RD map.  
Before running tensor2metric, I do preprocessing using these step

BET DTI image → denoise → eddy current correction → bias correction  
After I run tensor2metric \<input\_image\> -fa \<output\_image\>

and the output image looks different from what we know…

Is that a command line error what I type? or just the image scale problem?

 ![Screen Shot 2021-07-20 at 5.45.10 PM](https://community.mrtrix.org/uploads/default/original/2X/b/b937fddffbee82fcd0340579067f787793305eb2.png)

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### Author: ![suren](https://community.mrtrix.org/user_avatar/community.mrtrix.org/suren/32/3215_2.png) [@suren](https://community.mrtrix.org/u/suren)
#### Post date: [July 20, 2021, 10:57am UTC](https://community.mrtrix.org/t/problem-about-tensor2metric-to-generate-rd-fa-adc-md-map/5066/2 "2021-07-20T10:57:08Z")

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Hi @CarlisleYun79,

If the background is what is troubling you, you may add -mask mask\_image of your whole brain while calculating fa from the tensor. [tensor2metric — MRtrix 3.0 documentation](https://mrtrix.readthedocs.io/en/latest/reference/commands/tensor2metric.html)

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### Author: ![maxpietsch](https://community.mrtrix.org/user_avatar/community.mrtrix.org/maxpietsch/32/25_2.png) [@maxpietsch](https://community.mrtrix.org/u/maxpietsch)
#### Post date: [July 23, 2021, 10:10am UTC](https://community.mrtrix.org/t/problem-about-tensor2metric-to-generate-rd-fa-adc-md-map/5066/3 "2021-07-23T10:10:24Z")

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See [The value of FA.nii.gz - #3 by jdtournier](https://community.mrtrix.org/t/the-value-of-fa-nii-gz/429/3) for an explanation of FA values larger than 1.

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### Author: ![jdtournier](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jdtournier/32/2594_2.png) [@jdtournier](https://community.mrtrix.org/u/jdtournier)
#### Post date: [July 23, 2021, 11:34am UTC](https://community.mrtrix.org/t/problem-about-tensor2metric-to-generate-rd-fa-adc-md-map/5066/4 "2021-07-23T11:34:35Z")

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That does look odd for an FA map… May I ask whether these were acquired on a Phillips system? If so, this could be related to [this issue](https://community.mrtrix.org/t/dwipreproc-eddy-error/913/13) – which I note we are not always able to detect correctly. If you can post the full output of `mrinfo <input image> -dwgrad`, we might be able to spot the issue if that’s what it is…

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### Author: ![bjeurissen](https://community.mrtrix.org/user_avatar/community.mrtrix.org/bjeurissen/32/28_2.png) [@bjeurissen](https://community.mrtrix.org/u/bjeurissen)
#### Post date: [July 23, 2021, 12:03pm UTC](https://community.mrtrix.org/t/problem-about-tensor2metric-to-generate-rd-fa-adc-md-map/5066/5 "2021-07-23T12:03:30Z")

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The above pipeline does not list the dwi2tensor command.

Could it be that you are u are applying tensor2metric directly on the DWI data?