# Fa\_template resolution **URL:** \ **Category:** Uncategorized\ **Created:** [August 22, 2018, 8:14pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856 "2018-08-22T20:14:37Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![zeydabadi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/zeydabadi/32/1425_2.png) [@zeydabadi](https://community.mrtrix.org/u/zeydabadi)\ **Post date:** [August 22, 2018, 8:14pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/1 "2018-08-22T20:14:38Z")
Hi, My DWI data has 2mm isotropic resolution but the fa\_template created by “dwiintensitynorm” has 2.2x2.3x2.3mm resolution. Why this happens and how can I modify it? Thanks, Mahmoud ---
**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:** [August 25, 2018, 7:00pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/2 "2018-08-25T19:00:12Z")
This is caused by the way we calculate the unbiased voxel-grid in case of rotated input images. You can find a discussion [here](https://github.com/MRtrix3/mrtrix3/issues/1037). `population_template` has a `-voxel_size` option to modify this behaviour but this option is not accessible from `dwiintensitynorm`. If you’re after an FA template with specific resolution, I’d convert the DWI images to FA images and create a population template using `population_template`. ---
**Author:** ![zeydabadi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/zeydabadi/32/1425_2.png) [@zeydabadi](https://community.mrtrix.org/u/zeydabadi)\ **Post date:** [August 27, 2018, 2:49pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/3 "2018-08-27T14:49:26Z")
Thanks, Max. I’d like to know more about how “population\_template” creates the template. Like what are the steps, what types of registrations are used … . Is there a document that explains those details? ---
**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:** [August 27, 2018, 4:15pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/4 "2018-08-27T16:15:02Z")
Not a document but `population_template` prints an overview of what it is going to perform as info messages to the terminal at the beginning of the processing. After initial alignment, the template is iteratively refined (“stages”) by registering each subject to the template, and averaging the transformed subject images to form a new template. Here is an overview of the registration stages performed by default, for more options see the [docs](https://mrtrix.readthedocs.io/en/latest/reference/scripts/population_template.html): ![image](https://community.mrtrix.org/uploads/default/original/2X/f/fb667c66d246e5bf240e6990e1256c8314936c61.png) ---
**Author:** ![zeydabadi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/zeydabadi/32/1425_2.png) [@zeydabadi](https://community.mrtrix.org/u/zeydabadi)\ **Post date:** [August 27, 2018, 5:54pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/5 "2018-08-27T17:54:47Z")
Thanks for your response, Max. 1- Would you please elaborate what does initial alignment do? 2- Is it possible to introduce an initial template to start with it? like with FSL fnirt and fnirt commands. 3- After creating the fa\_template using the “population\_template”, I’d like to register the individual T2 images to that template. What’s the best way to do that? ---
**Author:** ![zeydabadi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/zeydabadi/32/1425_2.png) [@zeydabadi](https://community.mrtrix.org/u/zeydabadi)\ **Post date:** [February 15, 2019, 5:48pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/6 "2019-02-15T17:48:40Z")
I’d like to know if someone has an answer to my third question here? ---
**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 17, 2019, 6:07am UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/7 "2019-03-17T06:07:01Z")
> 3- After creating the fa\_template using the “population\_template”, I’d like to register the individual T2 images to that template. What’s the best way to do that? As always, I encourage distinction between _registration_ and _transformation_. If you have FA and T2-weighted images aligned for individual subjects, and you perform registration of subject FA images to a template (and either preserve the transformations estimated during the template generation procedure, or post-hoc explicitly register each subject’s FA image to the template FA image), then you can apply that same _transformation_ to the subject’s T2-weighted data, and it will undergo the same spatial transformation as that estimated to be optimal for moving the subject’s anatomy into the template space. Performing _registration_ between a subject image of one modality and a template image of another modality may be _possible_, but is generally best avoided. It is better IMO to do that inter-modality registration in the context of images corresponding to an individual subject, as that way the transformation is rigid only and therefore the complexity involved in measuring spatial correspondence between images with different contrasts is easier to manage. ---
**Author:** ![zeydabadi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/zeydabadi/32/1425_2.png) [@zeydabadi](https://community.mrtrix.org/u/zeydabadi)\ **Post date:** [June 25, 2019, 8:15pm UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/8 "2019-06-25T20:15:35Z")
Hi Max, Would you be able to tell me how the first step of template building works? what is exactly the initial alignment? i.e. alignment to what? Thank you, Mahmoud ---
**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:** [June 26, 2019, 10:00am UTC](https://community.mrtrix.org/t/fa-template-resolution/1856/9 "2019-06-26T10:00:10Z")
The `-initial_alignment` option in `population_template` performs translation of all images to a common central point calculated using the image intensity (“mass”) or the image centre (“geometric”). After that, the images are averaged which forms the initial template to which each image is registered before updating the template.