# Creating masked nifti from ROI

**URL:** <https://discourse.slicer.org/t/creating-masked-nifti-from-roi/10539>\
**Category:** Support\
**Created:** [March 4, 2020, 1:22pm UTC](https://discourse.slicer.org/t/creating-masked-nifti-from-roi/10539 "2020-03-04T13:22:54Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![joelyss](https://avatars.discourse-cdn.com/v4/letter/j/53a042/32.png) [@joelyss](https://discourse.slicer.org/u/joelyss)\
**Post date:** [March 4, 2020, 1:22pm UTC](https://discourse.slicer.org/t/creating-masked-nifti-from-roi/10539/1 "2020-03-04T13:22:54Z")

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Software version: 3D Slicer 4.10.2

I would like to draw an ROI on a ACPC transformed dataset, then create a binary mask of that ROI whee everything inside has a value of 1 and zeroes outside, and to have the same dimensions as the original nifti T1 dataset i.e. possibly requiring an invert transform. So I can take this nifti mask out of 3D slicer and use it in our current mrtrix3 processing pipeline.

I’m having a few issues doing this and following previous similar threads and online tutorials have not managed to figure this out.

My workflow currently:

- load in data & create models
- perform ACPC transform to data
- draw an ROI (that measures 4x4x6 mm3 in the ACPC transformed plane)

Then I get stuck. I have tried using the crop volume module and the mask scalar volume modules but I cannot seem to get what I am after.

Any help appreciated, many thanks,  
Joely

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 5, 2020, 5:26am UTC](https://discourse.slicer.org/t/creating-masked-nifti-from-roi/10539/2 "2020-03-05T05:26:47Z")

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You can draw ROI on an image using Segment Editor module (for example, using scissors or paint effects,or any of the automated tools), convert it to labelmap (by right-clicking on the segmentation in Data module), and save the labelmap as nifti.

If you want to draw an ROI with a specific shape and size then you can write a very simple scripted module, which takes markup points/lines as inputs to position a model node, then on the click of a button, it converts it to segmentation node, and then exports it as a labelmap. The module can also launch mrtrix3 processing and visualize the results in Slicer - all by a single click. The programming effort is probably a few hours for someone who is already familiar Slicer programming and maybe a few days for someone who is familiar with VTK, Python, and Qt but does not know anything about Slicer yet. See this [tutorial](https://www.slicer.org/wiki/Documentation/Nightly/Training#PerkLab.27s_Slicer_bootcamp_training_materials) to get started - and feel free to ask here if you have any questions.

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**Author:** ![joelyss](https://avatars.discourse-cdn.com/v4/letter/j/53a042/32.png) [@joelyss](https://discourse.slicer.org/u/joelyss)\
**Post date:** [March 12, 2020, 1:53pm UTC](https://discourse.slicer.org/t/creating-masked-nifti-from-roi/10539/3 "2020-03-12T13:53:29Z")

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Thank you for getting back to me !

I struggled to get it to work following the segmentation editor module. But I did figure out a way to do what I needed, so here it is if this helps future visitors:

I drew my ROI, in whichever way would work for you, as mine is based off of distances from landmarks and specific measurements (in mm) I found it easiest using the **‘Annotations’** module and using the ruler, fudicial and ROI tools.

Then to convert this to a model I used the **‘Markups to Model’** module.

This was possible as my ROI was a simple cuboid. I could locate the base slice, use the fudicial tool to mark out each corner of the ROI, scroll to the top slice of the ROI and draw fudicials on the 4 corners again.

Then I opened the **‘Data’** module, right clicked on the new ROI model and saved the model as a nii file.

Then checking the result in ImageJ I could see that even though I had performed an ACPC transform on the data in Slicer, it wasn’t ‘hardened’ and therefore the ROI was in the correct (original) space and I did not need to perform an invert transform.

Thanks for the tips on automation. This is something I will look into and go through the tutorial as this will really streamline my process.

Many thanks for the help,  
Joely