# Registering T1 image with AAL atlas intensity values changes

**URL:** https://community.mrtrix.org/t/registering-t1-image-with-aal-atlas-intensity-values-changes/3263
**Category:** Uncategorized
**Created:** [February 5, 2020, 7:32am UTC](https://community.mrtrix.org/t/registering-t1-image-with-aal-atlas-intensity-values-changes/3263 "2020-02-05T07:32:57Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![Asma\_Shaheen](https://community.mrtrix.org/user_avatar/community.mrtrix.org/asma_shaheen/32/2426_2.png) [@Asma\_Shaheen](https://community.mrtrix.org/u/Asma_Shaheen)
#### Post date: [February 5, 2020, 7:32am UTC](https://community.mrtrix.org/t/registering-t1-image-with-aal-atlas-intensity-values-changes/3263/1 "2020-02-05T07:32:57Z")

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I performed following steps

1. register T1 image to MNI space and compute the transformation matrix
2. then take the inverse of that matrix
3. apply registration using inverse matrix to AAL atlas and tranform it into my subject space (T1 space)
4. now i am overlapping mask (tumor mask) with this atlas based image  
tumor mask has three different labels. but in AAL atlas space intensity values has been changed so how i can get three different ROI based on tumor mask?

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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: [February 5, 2020, 1:29pm UTC](https://community.mrtrix.org/t/registering-t1-image-with-aal-atlas-intensity-values-changes/3263/2 "2020-02-05T13:29:13Z")

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I suspect you need to use nearest neighbour interpolation in step 3. (`-interp nearest` option for `mrtransform`).

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### Author: ![Asma\_Shaheen](https://community.mrtrix.org/user_avatar/community.mrtrix.org/asma_shaheen/32/2426_2.png) [@Asma\_Shaheen](https://community.mrtrix.org/u/Asma_Shaheen)
#### Post date: [February 5, 2020, 8:13pm UTC](https://community.mrtrix.org/t/registering-t1-image-with-aal-atlas-intensity-values-changes/3263/3 "2020-02-05T20:13:25Z")

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I tried it by using nn interpolation too. but the result is same.

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### Author: ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)
#### Post date: [March 1, 2020, 4:54am UTC](https://community.mrtrix.org/t/registering-t1-image-with-aal-atlas-intensity-values-changes/3263/4 "2020-03-01T04:54:29Z")

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I think there may actually be two separate questions embedded in one statement:

1. 

> transform it into my subject space … intensity values has been changed

2. 

> mask (tumor mask) … how i can get three different ROI based on tumor mask?

@maxpietsch’s response addresses specifically point 1: If you have an image that contains unique integer labels, you need to use nearest-neighbour interpolation at the re-gridding step in order to preserve those values.

For point 2, it sounds like you have a _single_ input parcellation image, containing _more than one_ unique integer label, and you instead wish to have multiple mask images, where each image contains only those voxels corresponding to one specific parcel index. If this is the case, this is a _separate step_ to the rest of the question, so got lost in communication. What you want in this case is the `-eq` operator in `mrcalc`. E.g. If you want a mask image that contains only those voxels where the value in the parcellation image is 3:

```auto
mrcalc tumour_parcels.mif 3 -eq tumour_index_3.mif

```

Rob

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### Author: ![Asma\_Shaheen](https://community.mrtrix.org/user_avatar/community.mrtrix.org/asma_shaheen/32/2426_2.png) [@Asma\_Shaheen](https://community.mrtrix.org/u/Asma_Shaheen)
#### Post date: [March 2, 2020, 6:57am UTC](https://community.mrtrix.org/t/registering-t1-image-with-aal-atlas-intensity-values-changes/3263/5 "2020-03-02T06:57:44Z")

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Thank you so much Rob. Issue has been solved.