# Bad registration of Freesurfer segmentation of the hippocampus

**URL:** <https://discourse.slicer.org/t/bad-registration-of-freesurfer-segmentation-of-the-hippocampus/1300>\
**Category:** SlicerSALT\
**Created:** [October 27, 2017, 8:11am UTC](https://discourse.slicer.org/t/bad-registration-of-freesurfer-segmentation-of-the-hippocampus/1300 "2017-10-27T08:11:13Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Olof](https://avatars.discourse-cdn.com/v4/letter/o/c57346/32.png) [@Olof](https://discourse.slicer.org/u/Olof)\
**Post date:** [October 27, 2017, 8:11am UTC](https://discourse.slicer.org/t/bad-registration-of-freesurfer-segmentation-of-the-hippocampus/1300/1 "2017-10-27T08:11:14Z")

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Hi,  
was wondering if anyone have experience with freesurfer segmentation of the hippocampus in SPHARM.

I tried various tricks but the registration really does not work. It is obvious that there are several irregularities of the shape from FS but I find it a bit strange that I cannot get the registration to work … as the overall shape is relatively similar between subjects.

So far i tried to increase or decreas spherical complexity 10 - 15 - 20 - did not work for any of these.

I also tried to use different subjects as reference for the registration (choosing one that seem to have a relatively regular shape).

Is there anything else that I can try?

best  
Olof

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**Author:** ![bpaniagua](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bpaniagua/32/20_2.png) [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Post date:** [October 27, 2017, 12:48pm UTC](https://discourse.slicer.org/t/bad-registration-of-freesurfer-segmentation-of-the-hippocampus/1300/2 "2017-10-27T12:48:39Z")

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Hi Olof,

Sorry this is being a challenge. Do you have an example snapshot on how the segmentation looks like?

Thank you,  
Bea

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**Author:** ![Olof](https://avatars.discourse-cdn.com/v4/letter/o/c57346/32.png) [@Olof](https://discourse.slicer.org/u/Olof)\
**Post date:** [November 1, 2017, 12:43pm UTC](https://discourse.slicer.org/t/bad-registration-of-freesurfer-segmentation-of-the-hippocampus/1300/3 "2017-11-01T12:43:34Z")

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![1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/9/997ef17122b4dafc05dbf0929a7845c252384ba7.png) ![2](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/6/b6e6f470b56cb3b4e1591449572f6d4e337d9620.png) ![3](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/0/80fae44b919c02fdc93bbdfc61cd2f89f8287829.jpeg)

So attached are some images … Highly irregular I admint - but I had hoped that the overall shape and curvature of the structure would make it possible to make an ok registration.