Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

Vertex order does not match across fsaverage resolutions
by Alexis Thual 22 Jul '23

22 Jul '23

External Email - Use Caution Hello! As suggested by the latest comment on this freesurfer github issue ( [ https://secure-web.cisco.com/1M0TqndURr2omFNMTTDpuWOzO_Vs7lJWAVS6xceXr6HXZ7… | https://secure-web.cisco.com/1M0TqndURr2omFNMTTDpuWOzO_Vs7lJWAVS6xceXr6HXZ7… ] ), I'm reaching out to you via email. In case that's useful, I'll copy the initial issue here: Problem As detailed in issue #3415 opened in nilearn, vertex order does not match across all fsaverage resolutions. I downloaded fsaverage 3 to 7 tarballs for the git annex of this repo and simply ran the following script to show that vertex order is not preserved across resolutions: # %% from nilearn import surface # %% fs3_path = "/home/alexis/singbrain/data/freesurfer_fsaverage/fsaverage3/surf/lh.pial" fs5_path = "/home/alexis/singbrain/data/freesurfer_fsaverage/fsaverage5/surf/lh.pial" fs7_path = "/home/alexis/singbrain/data/freesurfer_fsaverage/fsaverage7/surf/lh.pial" fs3_coordinates, fs3_faces = surface.load_surf_mesh(fs3_path) fs5_coordinates, fs5_faces = surface.load_surf_mesh(fs5_path) fs7_coordinates, fs7_faces = surface.load_surf_mesh(fs7_path) # %% print(fs3_coordinates[:5]) print(fs5_coordinates[:5]) print(fs7_coordinates[:5]) Output: [[-3.87359581e+01 -1.93433647e+01 6.72201385e+01] [-9.71759605e+00 -9.23328686e+00 4.65803757e+01] [-2.40194092e+01 4.31147995e+01 2.39262428e+01] [-5.98615112e+01 4.93119545e-02 8.97464848e+00] [-5.06454735e+01 -4.94050064e+01 4.78137321e+01]] [[-3.87359581e+01 -1.93433647e+01 6.72201385e+01] [-1.66624870e+01 -6.90612259e+01 6.12812729e+01] [-9.71761799e+00 -9.23326397e+00 4.65803413e+01] [-2.40194283e+01 4.31148720e+01 2.39262142e+01] [-5.98614998e+01 4.92927618e-02 8.97456360e+00]] [[-3.87359581e+01 -1.93433647e+01 6.72201385e+01] [-1.66624680e+01 -6.90612564e+01 6.12812119e+01] [-9.71762943e+00 -9.23325062e+00 4.65803223e+01] [-2.40194435e+01 4.31149139e+01 2.39261990e+01] [-5.98614883e+01 4.92815673e-02 8.97451496e+00]] Here, we see that the second vertex of fsaverage3 doesn't match that of fsaverage 5 and 7. I did some more extensive testing and it seems to me that: fsaverage 5, 6, 7 have consistent vertex order fsaverage 3 and 4's vertex order is different from 5, 6, 7 but can be reworked to be consistent, using a procedure I detailed in nilearn issue #3415 ( [ https://secure-web.cisco.com/1MUOQFQrlxwxUt85m4623j9t2ExzEpzjIm1YZnc6mKLXnd… | https://secure-web.cisco.com/1MUOQFQrlxwxUt85m4623j9t2ExzEpzjIm1YZnc6mKLXnd… ] ) Suggestion Maybe we should reorder fsaverage 3 and 4's vertices for all maps, what so you think? Thank you for the great software anyways! ☺️ Warm regards, Alexis

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Sulcal depth maps and pli de passage
by Federica Santacroce 21 Jul '23

21 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I used the sulcal depth maps superimposed on inflated images (setting colour depth =< 0) to define the morphological sulcal pattern (continuous vs. interrupted). Is this method useful for detecting pli de passage that may be buried deep in the depth of sulcus? [image: sulc.png] In this figure, is it correct to say that when two dark grey segments are adjacent, the sulcus is continuous (e.g. intraparietal sulcus)? On the other hand, when two dark grey segments are separated by a gyrus (light grey), can the sulcus be defined as interrupted (e.g. post-central sulcus)? Thanks in advance, Federica Santacroce

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Re: [Freesurfer] FreeSurfer 7.4.1 release changed?
by fsbuild 20 Jul '23

20 Jul '23

External Email - Use Caution  I think a change was made to the privileges on a single file in the archive.  Gzip subsequently may have changed the modification time in the updated archive and so the checksums could be different.  The checksums listed on the release page are up to date for 7.4.1 under, https://secure-web.cisco.com/1O7GIKohY89IzvrMFWBZrXhqN4gxL7jax2… - R. On Jul 20, 2023, at 18:13, Carlos Bederián <carlos.bederian(a)unc.edu.ar> wrote:        External Email - Use Caution        Hi, I have a question about the FreeSurfer 7.4.1 release. A couple weeks ago I added 7.4.1 along with its sha256 checksum to spack (which uses the centos7 binaries atm) after checking the md5 hash that is provided on the downloads page. The sha256 was independently confirmed by a spack maintainer so I believe that the checksums I had were correct at the time.This week, while trying to install 7.4.1 from spack, the sha256 checksum failed so I checked the md5sum against the one published in the downloads again and it matched. Has the tarball for 7.4.1 been switched intentionally without notice?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

FreeSurfer 7.4.1 release changed?
by Carlos Bederián 20 Jul '23

20 Jul '23

External Email - Use Caution Hi, I have a question about the FreeSurfer 7.4.1 release. A couple weeks ago I added 7.4.1 along with its sha256 checksum to spack (which uses the centos7 binaries atm) after checking the md5 hash that is provided on the downloads page. The sha256 was independently confirmed by a spack maintainer so I believe that the checksums I had were correct at the time. This week, while trying to install 7.4.1 from spack, the sha256 checksum failed so I checked the md5sum against the one published in the downloads again and it matched. Has the tarball for 7.4.1 been switched intentionally without notice?

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online freesurfer
by Gonzalo Rojas Costa 20 Jul '23

20 Jul '23

External Email - Use Caution Hi: Is there a freesurfer-based system that allows processing online an mprage image? Sincerely, Gonzalo Rojas Costa

2 1

freesurfer overlay function
by Magang Visa 20 Jul '23

20 Jul '23

External Email - Use Caution can we use freeview for comparing 2 MRI in a overlaying 3D model in one windows ? best regards

2 1

Missing chunk in wmparc
by Fahad Hannan 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, Looking at the wmparc.mgz file, there is a chunk in the top right frontal region that does not show up as part of the segmentation. I figured I needed to add control points through Freeview in case the chunk was not included as part of the brain. However, in Freeview it shows it included in the segmentation. Images attached show the brain in 3Dslider where the chunk is not segmented, and Freeview showing rl/lh.white and rl/lh.pial overlayed. Regards, Fahad

2 1

WM Hypointensities
by Andrew Dedinas Geoly 20 Jul '23

20 Jul '23

External Email - Use Caution Hi Freesurfer experts! I am hoping to extract the wm-hypointensity data from some recon-all-clinical runs. I was able to extract aseg.stats information correctly but noticed there was no information regarding the wm-hypointensities. Is this supported by recon-all-clinical? Best, Andrew --- Andrew D. Geoly, MS Research Data Analyst 1 Brain Stimulation Lab Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine

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Calculate cortical thickness of a volumetric ROI
by Carlos Alcocer 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using https://secure-web.cisco.com/1Z5OP8XDp2iTZo4YMybrzCFH9SwKBzyQx9vsSEFhl_f6qf… as a guide. Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels. Thank you, Carlos

3 3

Aparc2aseg citation
by Alberto Del Cerro Leon 20 Jul '23

20 Jul '23

External Email - Use Caution Hi FS team, for my line of research I have used aparc2aseg with the --labelwm --hypo-as-wm option to obtain wm measurements from a custom atlas of the brain lobes. However I don't know how I should cite this method as the aparc2aseg documentation does not specify. Thanks in advance

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Freesurfer July 2023