Hello, I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz" file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview.
Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export? Thank you for all your help, Angelique
Dear Angelique I’m not a 3DSlicer expert but you can extract the regions with mri_extract_region, turn them into stl meshes with mri_mc, and possibly smooth them a bit with mris_smooth Cheers, /E
Juan Eugenio Iglesias http://www.jeiglesias.com
On Sep 24, 2022, at 16:15, Paulk, Angelique C.,PHD <APAULK@mgh.harvard.edumailto:APAULK@mgh.harvard.edu> wrote:
Hello, I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz" file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview.
Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export? Thank you for all your help, Angelique _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello, Thank you very much for getting back to me. I keep trying to find 'mri_extract_region' and I can't find anything on it (we have Freesurfer 7 installed). I did find I could get .stl files to work with using the below commands (mris_smooth did not seem to work).
current commands (done per nucleus label): mri_extract_label ThalamicNuclei.v12.T1.mgz 8133 Left-VPL.nii mri_mc Left-VPL.nii 128 Left-VPL.stl
However, the exported volumes and .stl files are not registered to the original T1.mgz output or the pial surfaces. Is there a command or option that I am missing to ensure that the output is all registered to the original volume or T1? I am guessing it is mri_convert but I am not clear on the transform file needed to register the ThalamicNuclei.v12.T1.mgz file to T1.mgz. It is clear Freeview does this automatically but, for electrode localization (intracranial recordings) and various measurements, I need to export the volumes and surfaces outside of FreeSurfer.
Thank you for any and all help, Angelique ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E.,PHD JIGLESIASGONZALEZ@mgh.harvard.edu Sent: Saturday, September 24, 2022 8:09 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Thalamic nucleus segmentation 3D export
Dear Angelique I’m not a 3DSlicer expert but you can extract the regions with mri_extract_region, turn them into stl meshes with mri_mc, and possibly smooth them a bit with mris_smooth Cheers, /E
Juan Eugenio Iglesias http://www.jeiglesias.com
On Sep 24, 2022, at 16:15, Paulk, Angelique C.,PHD <APAULK@mgh.harvard.edumailto:APAULK@mgh.harvard.edu> wrote:
Hello, I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz" file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview.
Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export? Thank you for all your help, Angelique _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Angelique, Are you using Freeview for visualization? If so, everything should overlap just right. If not: can you please send us a capture? Cheers, /Eugenio
Juan Eugenio Iglesias http://www.jeiglesias.com
On Oct 8, 2022, at 22:58, Paulk, Angelique C.,PHD <APAULK@mgh.harvard.edumailto:APAULK@mgh.harvard.edu> wrote:
Hello, Thank you very much for getting back to me. I keep trying to find 'mri_extract_region' and I can't find anything on it (we have Freesurfer 7 installed). I did find I could get .stl files to work with using the below commands (mris_smooth did not seem to work).
current commands (done per nucleus label): mri_extract_label ThalamicNuclei.v12.T1.mgz 8133 Left-VPL.nii mri_mc Left-VPL.nii 128 Left-VPL.stl
However, the exported volumes and .stl files are not registered to the original T1.mgz output or the pial surfaces. Is there a command or option that I am missing to ensure that the output is all registered to the original volume or T1? I am guessing it is mri_convert but I am not clear on the transform file needed to register the ThalamicNuclei.v12.T1.mgz file to T1.mgz. It is clear Freeview does this automatically but, for electrode localization (intracranial recordings) and various measurements, I need to export the volumes and surfaces outside of FreeSurfer.
Thank you for any and all help, Angelique ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E.,PHD <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> Sent: Saturday, September 24, 2022 8:09 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Thalamic nucleus segmentation 3D export
Dear Angelique I’m not a 3DSlicer expert but you can extract the regions with mri_extract_region, turn them into stl meshes with mri_mc, and possibly smooth them a bit with mris_smooth Cheers, /E
Juan Eugenio Iglesias http://www.jeiglesias.comhttp://www.jeiglesias.com/
On Sep 24, 2022, at 16:15, Paulk, Angelique C.,PHD <APAULK@mgh.harvard.edumailto:APAULK@mgh.harvard.edu> wrote:
Hello, I apologize if this has been answered before though I could not find this specific information in the archives. We are hoping to export the Thalamic nuclei segmentations to 3D volumes outside of Freeview/Freesurfer (e.g. .stl or other options) to perform a number of calculations in python or Matlab or visualize in Blender. I have been able to use 3DSlicer and get segmentation and 3D renders by importing the "aparc.DKTatlas+aseg.mgz" file and export .stl files in 3DSlicer, but, when I import the "ThalamicNuclei.v12.T1.FSvoxelSpace.mgz" file, it is only showing the entire thalamus as a mask in 3DSlicer though the nuclei are segmented in Freeview.
Is there another type of export from FreeSurfer that would allow this type of saved volume/surface export? Thank you for all your help, Angelique _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Iglesias Gonzalez, Juan E.,PHD -
Paulk, Angelique C.,PHD