Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

FS 7.2.0 VM pass code
by Dina V. Popovkina 24 Jul '23

24 Jul '23

External Email - Use Caution Hi Freesurfer team, I'm looking for the pass code for the VM image with the 7.2.0 version of FreeSurfer. Many thanks, Dina Dina V. Popovkina, Ph.D. Postdoctoral Scientist, Vision + Cognition Group Department of Psychology, University of Washington

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Any chance at all for an official proper fix for Freesurfer on FIPS?
by Salomon, Ryan 24 Jul '23

24 Jul '23

External Email - Use Caution Hello! I'm trying to support our users who use Freesurfer on our systems, but we are trying to keep to a rollout of FIPS, without the need to employ any hacks or the like, and I don't believe non-FIPS is an option on our systems. We still encounter the crypt() error on Freesurfer versions greater than 7.1.1, and again, non-FIPS is likely not an option. There is an environment variable workaround that has been mentioned elsewhere and it doesn't seem to be working for me for mri_deface at least, and again, I really would like to see a word about a proper solution.

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Possible bug: recon-all -i $T1 -T2 $T2 -autorecon1 attempts to run -T2pial
by Christopher Markiewicz 24 Jul '23

24 Jul '23

External Email - Use Caution Hi all, This is a reproduction of GitHub issue 1010. There is a section of recon-all (L5927-5930 in current dev) that states: # MOD: turn on T2/FLAIR pial editing when FLAIR specified # This can backfire, eg, if not all the preceeding steps # are included set DoT2pial = 1; This seems an intentional decision to make -T2 activate -T2pial (and similar for -FLAIR), which I suppose is a response to people running `recon-all -i $T1 -T2 $T2 -all` without `-T2pial`. However, it also activates with -autorecon1 and -autorecon2, which will not run -pial before -T2pial. Would you all consider this a bug or a caveat emptor kind of situation? Would it make sense to add the following to -autorecon1 and -autorecon2 (hopefully this formats okay)? diff --git a/scripts/recon-all b/scripts/recon-all index 4b98118264..0655097ab9 100755 --- a/scripts/recon-all +++ b/scripts/recon-all @@ -6869,6 +6869,7 @@ while( $#argv != 0 ) breaksw case "-autorecon1": + set DoT2pial = 0; set DoCreateBaseInput = 1; set DoMotionCor = 1; set DoTalairach = 1; @@ -6911,6 +6912,7 @@ while( $#argv != 0 ) set DoRemoveNeck = 0; set DoSkullLTA = 0; set DoSegStats = 0; + set DoT2pial = 0; set DoCANormalize = 1; set DoGCAReg = 1; set DoCALabel = 1; In any case, I am now adding -noT2pial and -noFLAIRpial to -T2 calls that aren't -all as well, which seems safe for writing commands that will work for both FreeSurfer 6 and 7. Thanks, Chris

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PetSurfer analisis whit another atlas
by Matteo Parodi 24 Jul '23

24 Jul '23

External Email - Use Caution Good morning. I try to use surfer analysis with another atas instead of the built-in one. I have an atlas in nifti or mgz format. I tried using it in gtmseg's --head option and it doesn't work, maybe due to normalization issues but I'm not sure. I tried to build the atlas with the utilities in https://secure-web.cisco.com/1npKm2rw7ypoDV5y3qkt0Aa0W2d4IRkHhrWfsjK3gU03P8… but i have problems to interfacing whit gca, gcs and annot file. I searched the mail archive and found no answer. Thank you very much for any input, Parodi.

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Request for 7 zip password VM_67
by Ynze Hokken 24 Jul '23

24 Jul '23

External Email - Use Caution Dear freesurfer expert, I just need a passcode to archive the zip folder for file FS_7_2_0_ubuntu_18_04_06.ova so that i can install a FreeSurfer vitual disk. Thanks, Ynze Hokken

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Re: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)
by Jackson Lee 23 Jul '23

23 Jul '23

External Email - Use Caution Hi Yujing, Thanks for your reply – I have a follow up query (see email thread below): I have both a cross-sectional aim and a longitudinal aim I am hoping to explore with FreeSurfer. While they are separate aims, some participants are present in both the cross-sectional and longitudinal arm. Currently I have run recon-all on all participants for my study using the standard recon-all command. As mentioned, I am hoping to do hippocampal subfield analysis (both cross-sectional and longitudinal). I have read both the hippocampal subfield and longitudinal pipelines available from FreeSurfer (linked below): https://secure-web.cisco.com/1_iq2Ortiz8d4uJhrtEXKZ_Row3SgFJsQNSJUW3b3hm3Fp… https://secure-web.cisco.com/1K3vQAJc_XjPimaagPX_W_n-ig3v4kt3fgvsYNoj9HGxxF… I was planning on running the longitudinal recon-all pipeline as it seems that running longitudinal pipeline allows for greater reliability as "the subject is used as their own control". But if I do this, then the subjects that are also in the cross-sectional arm will potentially have different outputs (even though they are the same scan) compared to outputs from the longitudinal pipeline. This would be the same for the subfield analysis. What is the best approach here? Would I be better off running all participants (even those with one T1-weighted scan) with the longitudinal pipeline so that every participant is treated the homogenously? Let me know if I need to clarify anything! Warm regards, Jack Hi Jack, Longitudinal recon-all pipeline is available in Freesurfer 7.3.2. To do longitudinal segmentation using the hippocampal subfield pipeline, it is a requirement that the data have been processed with the longitudinal stream Freesurfer. Best, Yujing From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Jackson Lee Sent: Wednesday, July 12, 2023 10:25 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2) External Email - Use Caution Hi there, I am hoping to process some longitudinal data using the longitudinal recon-all pipeline available in FreeSurfer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalChangeLog<https://secure-web.cisco.com/1Y9uqixBqGC2B0XHSMg2zr4QS96oUVSkkZcMdhRqdEkVD1…> Will this pipeline work for FreeSurfer v7.3.2? I cannot see any resources to suggest this is the case. Additionally, I am hoping to conduct some longitudinal analysis using the hippocampal subfield pipeline: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOf…<https://secure-web.cisco.com/1ILqdmv74otr5LeRS7UQz83p5UDddkh5pv-Luvs5PHnW-6…> Would the best course of action be to run recon-all with the longitudinal pipeline first (assuming it is applicable for freeSurfer v7.3.2) and then use the longitudinal command for post-hoc subfield analysis?: segmentHA_T1_long.sh <baseID> [SUBJECTS_DIR] Thank you, Jack

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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

3 3

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

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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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