Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Hippocampal segmentation
by Alberto Del Cerro Leon 01 Mar '21

01 Mar '21

External Email - Use Caution Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf and editing the labels manually. However when I was editing the labels in tksurfer the hippocampal field is quite bad. I tried to look the segmentation used by you in labels but I didn't find it. How could I segment the Hippocampus????

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Installing freesurfer 6 in a preexisting conda environment
by Bruno Mansur 01 Mar '21

01 Mar '21

External Email - Use Caution Dear community members, I created a conda environment for installing MNE. Now I want to install freesurfer in this same environment to use freesurfer in combination with MNE. Does anyone have already installed and configured freesurfer in an environment and could give me some support with it? The mailing list has no entries related to 'conda environment' and the freesurfer installation guide webpage has no instructions related to this. I would appreciate any help, Best regards -- *Bruno*

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mincRead error
by Michele Valotti 01 Mar '21

01 Mar '21

External Email - Use Caution Hi all, I am running long FreeSurfer and after successfully testing it on my local machine I tried to run it on a server (which should however have the same FreeSurfer version and setup), but I am getting this error mri_convert ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.533/nu1.mnc orig_nu.mgz --like orig.mgz --conform ncopen: filename "./tmp.mri_nu_correct.mni.533/nu1.mnc": Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.533/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.533/nu1.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.533/nu1.mnc... Linux 18e36413df0c 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 UTC 2020 x86_64 GNU/Linux recon-all -s base_freesurfer exited with ERRORS at Fri Feb 5 17:45:34 UTC 2021 Any idea what the cause of this might be? Thank you!

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FreeSurfer 7 vs FreeSurfer 6 surface differences
by Mike Schmidt 01 Mar '21

01 Mar '21

External Email - Use Caution I have written a script that reads the binary representations of the vertices and faces from FreeSurfer's surf/{l,r}h.pial files and saves them out unchanged to stl and obj file formats for 3D rendering. I have used it with FreeSurfer 6 and several MRI images, everything working fine. Processing the identical input, a single T1-weighted MPRAGE MRI, FreeSurfer 7 works great and finishes faster than FreeSurfer 6, but we see strange aliasing on the 3D objects. The aliasing is identical if I avoid all of my own code and use mris_convert (from either FreeSurfer version) to generate an stl file from the pial file. I've spent a lot of time debugging, messing with different materials and textures, generating vertex normals at different stages, but I can't find anything that makes any difference except the FreeSurfer version. I have seen several items in the release notes ( https://secure-web.cisco.com/1NYZrvHyVXqxTpZBiwiJ49J4EeeNWwqM6oBe0m-ipN8Gos…) that may be related, but I'm not sure how to go about investigating them. Left cortex images are included, with links if they don't show up in the email, of the same brain processed with FS6 and FS7. These are rendered in Firefox with the three.js library. FreeSurfer 6.0.0 works well with a smooth surface ( https://secure-web.cisco.com/1eQ5Q62ZQtG-RYtwAFFKvhYNEYp7A20Vte8M_v6fEXDVss…) This image is of surf/lh.pial with 149,968 vertices and 299,932 faces. [image: rh_pial_oblique_from_fs6.png] FreeSurfer 7.1.1 results in the same size and shape cortex, but renders strangely with mottled shading of triangles. ( https://secure-web.cisco.com/1JB4zyZhlTjmxoItAOFNb40IoMYhEZt8T-O0MINoKqg8cl…) This image is from the same T1 image as above, but processed with FS7, resulting in 147,292 vertices and 294,580 faces. [image: rh_pial_oblique_from_fs7.png] I'm out of ideas, and the only difference I can find is FreeSurfer version, so thank you to anyone who can point me in the right direction to fix this issue. Mike Schmidt

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Freesurfer March 2021