# Batch co-registration using BRAINSfit (script)

**URL:** <https://discourse.slicer.org/t/batch-co-registration-using-brainsfit-script/24285>\
**Category:** Development\
**Tags:** registration, brainsfit, python, batch\
**Created:** [July 12, 2022, 1:08pm UTC](https://discourse.slicer.org/t/batch-co-registration-using-brainsfit-script/24285 "2022-07-12T13:08:05Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![dokay1](https://avatars.discourse-cdn.com/v4/letter/d/b4bc9f/32.png) [@dokay1](https://discourse.slicer.org/u/dokay1)\
**Post date:** [July 12, 2022, 1:08pm UTC](https://discourse.slicer.org/t/batch-co-registration-using-brainsfit-script/24285/1 "2022-07-12T13:08:05Z")

</div>

For those looking for a script for Batch co-reg. You still have to add the string “FIXED” (case sensitive) to the name of the volume you want to use as the reference/fixed volume for co-registration.

```auto
PoolOfVolumes = getNodesByClass('vtkMRMLScalarVolumeNode')
FixedVol = getNode('*FIXED*')
for MovingVol in PoolOfVolumes:
    slicer.util.selectModule('BRAINSFit')
    brainsFit = slicer.modules.brainsfit   
    parametersRigid = {}
    parametersRigid["fixedVolume"] = FixedVol.GetID()
    parametersRigid["movingVolume"] = MovingVol.GetID()
    parametersRigid["outputVolume"] = MovingVol.GetID()
    parametersRigid["useRigid"] = True
    parametersRigid["initializeTransformMode"] = "useGeometryAlign"
    parametersRigid["samplingPercentage"] = 0.02
    cliBrainsFitRigidNode = slicer.cli.run(brainsFit, None, parametersRigid)

```

Tested and works on Slicer 5.0.2 r30822 / a4420c3 on MacOS 12.4 using brain MRIs.

Cheers,

Dave

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<div class="post-metadata">

**Author:** ![koeglfryderyk](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/koeglfryderyk/32/14638_2.png) [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Post date:** [September 9, 2024, 8:05am UTC](https://discourse.slicer.org/t/batch-co-registration-using-brainsfit-script/24285/2 "2024-09-09T08:05:36Z")

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> [@dokay1](#):
>
> `brainsfit`

Where can I find all the parameter names (like samplingPercentage etc)?

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<div class="post-metadata">

**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:** [September 9, 2024, 2:36pm UTC](https://discourse.slicer.org/t/batch-co-registration-using-brainsfit-script/24285/3 "2024-09-09T14:36:54Z")

</div>

[https://slicer.readthedocs.io/en/latest/user\_guide/modules/brainsfit.html](https://slicer.readthedocs.io/en/latest/user_guide/modules/brainsfit.html)

and

> <https://github.com/BRAINSia/BRAINSTools/blob/main/BRAINSFit/BRAINSFit.xml>