# \#freesurfer

**URL:** https://discourse.slicer.org/tag/freesurfer/257.md

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## [Not able to load Freesurfer Model (lh.pial) on Slicer 5.8.1](https://discourse.slicer.org/t/not-able-to-load-freesurfer-model-lh-pial-on-slicer-5-8-1/43761)

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**Author:** [@justomont](https://discourse.slicer.org/u/justomont)\
**Replies:** 4\
**Last updated:** [July 22, 2025, 9:31am UTC](https://discourse.slicer.org/t/not-able-to-load-freesurfer-model-lh-pial-on-slicer-5-8-1/43761 "2025-07-22T09:31:30Z")

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I’m trying to load a FreeSurfer model (lh.pial) programmatically through a scripted module but I’m not achieving it. I’ve tried: fsImporterLogic = slicer.util.getModuleLogic('FreeSurferImporter') volumeNode = fsImporte…

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## [SlicerFreeSurfer runs out of memory to load wmparc.mgz](https://discourse.slicer.org/t/slicerfreesurfer-runs-out-of-memory-to-load-wmparc-mgz/42608)

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**Author:** [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Replies:** 1\
**Last updated:** [April 17, 2025, 8:05pm UTC](https://discourse.slicer.org/t/slicerfreesurfer-runs-out-of-memory-to-load-wmparc-mgz/42608 "2025-04-17T20:05:30Z")

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Slicer-5.6.1 @pieper asked us to use SlicerFreeSurfer extension. We installed it. But when trying to load a wmparc.mgz file, we get the following: Console error is: Slicer has caught an application error, please s…

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## [Missing “Reference Volume” option in FreeSurfer Importer (it looks like version 5.6 onwards)](https://discourse.slicer.org/t/missing-reference-volume-option-in-freesurfer-importer-it-looks-like-version-5-6-onwards/35977)

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**Author:** [@Nis175](https://discourse.slicer.org/u/Nis175)\
**Replies:** 4\
**Last updated:** [May 16, 2024, 9:17pm UTC](https://discourse.slicer.org/t/missing-reference-volume-option-in-freesurfer-importer-it-looks-like-version-5-6-onwards/35977 "2024-05-16T21:17:20Z")

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Dear 3D Slicer Team, I have noticed that the “Reference Volume” option available in version 5.4.0 of the FreeSurfer importer has been removed in the latest versions, including 5.6.2. Please see the attached screenshots…

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## [Misalignment between Freesurfer brain segmentation and original T1 images](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524)

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**Author:** [@pablomac7](https://discourse.slicer.org/u/pablomac7)\
**Replies:** 2\
**Last updated:** [April 16, 2024, 12:20pm UTC](https://discourse.slicer.org/t/misalignment-between-freesurfer-brain-segmentation-and-original-t1-images/35524 "2024-04-16T12:20:44Z")

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Slicer version: 5.6.1 Hello, I am having problems when exporting a brain segmentation as a .seg.nrrd file, previously imported into 3D Slicer from Freesurfer. When I import the segmentation and the original MRI images …

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## [How to load FreeSurfer surface files in correct position using Python script](https://discourse.slicer.org/t/how-to-load-freesurfer-surface-files-in-correct-position-using-python-script/13183)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 4\
**Last updated:** [February 28, 2024, 10:17pm UTC](https://discourse.slicer.org/t/how-to-load-freesurfer-surface-files-in-correct-position-using-python-script/13183 "2024-02-28T22:17:17Z")

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Hello, am writing a module which uses FreeSurfer segmentations and surface files. Empirically and based on another discourse post (Nifti file and freesurfer pial file mismatch in slicer) I had previously developed a tra…

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## [FreeSurfer volumetric analysis](https://discourse.slicer.org/t/freesurfer-volumetric-analysis/34197)

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**Author:** [@Nicolas\_Fuentes](https://discourse.slicer.org/u/Nicolas_Fuentes)\
**Replies:** 1\
**Last updated:** [February 7, 2024, 11:43pm UTC](https://discourse.slicer.org/t/freesurfer-volumetric-analysis/34197 "2024-02-07T23:43:10Z")

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Hi everyone, I’m new to Slicer and I have some questions about the software’s capabilities for volumetric analysis. I work with neuroimages and I have patients processed with FreeSurfer. With that said, what I want to do…

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## [Error loading freesurfer segmentation](https://discourse.slicer.org/t/error-loading-freesurfer-segmentation/32674)

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**Author:** [@Maurilio\_Genovese](https://discourse.slicer.org/u/Maurilio_Genovese)\
**Replies:** 6\
**Last updated:** [November 11, 2023, 2:53pm UTC](https://discourse.slicer.org/t/error-loading-freesurfer-segmentation/32674 "2023-11-11T14:53:49Z")

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Hi, I am facing the same problem. When I try to load a freesurfer segmentation (a standard aparc+aseg.mgz) on Ubuntu (either using the importer interface, the load volume interface or a slicerpython command) I will get t…

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## [Infant Freesurfer .pial and .sulc not loadable onto 3d Slicer 5.3.0](https://discourse.slicer.org/t/infant-freesurfer-pial-and-sulc-not-loadable-onto-3d-slicer-5-3-0/32411)

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**Author:** [@orocchio-giordano](https://discourse.slicer.org/u/orocchio-giordano)\
**Replies:** 1\
**Last updated:** [October 25, 2023, 4:26pm UTC](https://discourse.slicer.org/t/infant-freesurfer-pial-and-sulc-not-loadable-onto-3d-slicer-5-3-0/32411 "2023-10-25T16:26:16Z")

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Hello! I am using clinical data processed through the infant\_recon\_pipeline in Freesurfer and I am receiving error messages when I try to load the pial surfaces and sulc scalar overlays into 3d Slicer. With previous da…

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## [Correct registration in Slicer output to Freesurfer](https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934)

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**Author:** [@Victor\_Zeng](https://discourse.slicer.org/u/Victor_Zeng)\
**Replies:** 1\
**Last updated:** [September 27, 2023, 5:29pm UTC](https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934 "2023-09-27T17:29:06Z")

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Hi all, for this project here, I am inputting into Slicer a brain image made in Freesurfer, namely the orig.mgz. Then I am managing manual segmentations done in Slicer using Segment Editor. Then I click on Export visible…

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## [New Extension: SlicerFreeSurfer](https://discourse.slicer.org/t/new-extension-slicerfreesurfer/12751)

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**Author:** [@Sunderlandkyl](https://discourse.slicer.org/u/Sunderlandkyl)\
**Replies:** 3\
**Last updated:** [March 8, 2023, 9:59pm UTC](https://discourse.slicer.org/t/new-extension-slicerfreesurfer/12751 "2023-03-08T21:59:29Z")

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We have added a new extension called SlicerFreeSurfer to the latest Slicer preview releases (4.11). This exension takes over handling FreeSurfer models/scalar overlay import from the 3D Slicer core, and adds support for…

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## [Nifti file and freesurfer pial file mismatch in slicer](https://discourse.slicer.org/t/nifti-file-and-freesurfer-pial-file-mismatch-in-slicer/11387)

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**Author:** [@Tutu](https://discourse.slicer.org/u/Tutu)\
**Replies:** 3\
**Last updated:** [March 8, 2023, 5:34am UTC](https://discourse.slicer.org/t/nifti-file-and-freesurfer-pial-file-mismatch-in-slicer/11387 "2023-03-08T05:34:07Z")

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Hi slicers, I tried to view several files that were built from Freesurfer (brain.mgz, l/rh.pial,l/rh.white). However, I found the surface of the pial could not match the outline of raw MRI images. I checked online and f…

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## [How to export Model Scalar data?](https://discourse.slicer.org/t/how-to-export-model-scalar-data/17810)

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**Author:** [@mgpoirot](https://discourse.slicer.org/u/mgpoirot)\
**Replies:** 6\
**Last updated:** [June 2, 2021, 3:44pm UTC](https://discourse.slicer.org/t/how-to-export-model-scalar-data/17810 "2021-06-02T15:44:27Z")

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I’m trying to work with FreeSurfer cortical scalar mappings. Luckily, Slicer is able to open these as ‘Freesurfer scalar overlay’ They can be applied to a model inside FreeSurfer. This is what it looks like I’m tr…

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## [Old FreeSurfer color lookup table](https://discourse.slicer.org/t/old-freesurfer-color-lookup-table/13184)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 4\
**Last updated:** [December 7, 2020, 10:05pm UTC](https://discourse.slicer.org/t/old-freesurfer-color-lookup-table/13184 "2020-12-07T22:05:55Z")

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In older Slicer releases, there was a color map called “FreeSurfer Labels”. In more recent nightly releases, this color map is gone, and I see new ones called “SPL-BrainAtlas-2009-ColorFile”, “SPL-BrainAtlas-2012-ColorF…

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## [Saved pial surface model reloads as invalid](https://discourse.slicer.org/t/saved-pial-surface-model-reloads-as-invalid/10268)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 6\
**Last updated:** [February 17, 2020, 6:33pm UTC](https://discourse.slicer.org/t/saved-pial-surface-model-reloads-as-invalid/10268 "2020-02-17T18:33:00Z")

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Hello, I use FreeSurfer to generate cortical surface models from a brain MR volume (outside of Slicer). Slicer can load the resulting surface files (lh.pial and rh.pial) as models and they seem to function as normal mod…

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## [Moving FreeSurfer support to an extension](https://discourse.slicer.org/t/moving-freesurfer-support-to-an-extension/9390)

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**Author:** [@Sunderlandkyl](https://discourse.slicer.org/u/Sunderlandkyl)\
**Replies:** 6\
**Last updated:** [December 5, 2019, 10:05pm UTC](https://discourse.slicer.org/t/moving-freesurfer-support-to-an-extension/9390 "2019-12-05T22:05:56Z")

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Hi All, Recently, we’ve been development on an extension to import FreeSurfer models in the correct coordinate system, as well as to import other files at the same time (segmentations, scalar overlay, etc.). As part of…