Freesurfer August 2024

freesurfer@nmr.mgh.harvard.edu

43 participants
58 discussions

Save (any/open) path in freeview
by Marianne Duyck 12 Aug '24

12 Aug '24

External Email - Use Caution Dear freesurfer experts, I am currently using freeview 7.2.0. I want to compare some area delineation from two conditions. To do that I wanted to extract vertices of an open path (some line drawn on an inflated surface) in these two conditions (so then I can systematically calculate distances between the two conditions). However I couldn’t find how to save (the vertices of) an open path. Did I miss how to do it? (If so how?) Is there another way to get the same information I am not aware of? Is the feature I’m looking for available in more recent versions? (If so what are the steps to get there?). Thanks in advance for your inputs! Marianne

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Patterned Recon-All Crashes on Version 7.1.1
by Emily Popa 12 Aug '24

12 Aug '24

External Email - Use Caution Hello, In the past few months I have observed a persistent issue when running recon-all (FreeSurfer version 7.1.1) on subjects whose pial and white matter surfaces have been edited by students in our lab (they would edit brainmask.mgz or wm.mgz, or add control points). The issue started around May of this year, prior to which I had frequently ran recon-all on edited cases without any issues using the same version of FreeSurfer, on the same system (a linux server running on AWS), using various configurations (ranging from an 8 CPU, 32 GB build to a 64 CPU 256 GB build), both with and without the -threads option + different values depending on the build. The problem is as follows: when I submit the cases in different terminals, one after another, using recon-all -s SubjectID/ -all -qcache, (tested with/without every reasonable -threads or -openmp option), the jobs get stuck on the same step and stop processing, but if I stagger them and leave sufficient time between when each is submitted, they will work as usual and complete without error. Even if I run just two cases on an excessively large server build relative to the processing requirements, they will still get stuck if I start the jobs right after each other (~30 seconds – several minutes). I’ve tried installing the same version of FreeSurfer in a different location, but have observed no change in this pattern of behavior. I asked our IT support to check if anything else had changed, and they reported that there was nothing they could think of that has changed from an infrastructure perspective (same server configuration), and that the only thing that had changed was the size of the hard drive a couple times. A very common step the jobs seem to get stuck is mri_em_reg+, and when I open the terminal, the last lines read “Nine parameter search. iteration # nscales = 1 . . .” at the bottom of the terminal followed by a line of asterisks (see screenshot below). [cid:image001.png@01DAEC7F.D0930A30] Here is an example of the output of top, which shows that all the recon jobs had a status of “sleeping” after 6+ hours of being submitted and were on the same step: [cid:image002.png@01DAEC80.2A8F89F0] Any suggestions/insight into what is happening here would be greatly appreciated, many thanks! Best, Emily S. Popa, M.S. Programmer Analyst I, Neuroimaging Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center 1301 20th St. #250 Santa Monica, CA. 90404 (408) 750-7971 (M) [cid3519*image001.jpg(a)01D7EC78.96AA1AC0]<https://www.linkedin.com/in/emilypopa/> [cid3519*image002.jpg(a)01D7EC78.96AA1AC0] <https://www.facebook.com/PacificNeuroscienceInstitute> [cid3519*image003.jpg(a)01D7EC78.96AA1AC0] <https://twitter.com/PacificNeuroPNI> [cid3519*image004.jpg(a)01D7EC78.96AA1AC0] <https://www.instagram.com/pacificneuro/> [cid3519*image005.jpg(a)01D7EC78.96AA1AC0] <https://www.pacificneuroscienceinstitute.org/brain-health/>

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mri_watershed Error: GLOBAL region of the brain empty !
by 李志豪 10 Aug '24

10 Aug '24

External Email - Use Caution 李志豪 2310117128(a)stu.pku.edu.cn Hello , freesurfer developers, I’m attempting to segment some brain mri data which is for training.But I encounter the following error: mri_watershed Error: GLOBAL region of the brain empty ! I have tried the possible resolution on freesurfer wiki but it does not work.I infer that the error happen in the fifth step-skull strip so I pre-finish this process by FSL bet.Unfortunately, it goes without effect.Can you offer some suggestions? I have attached recon-all.log if it’s of any use. 1):version—freesurfer-macos-darwin-x86_64-7.4.1 2):platform:mac0s darwin 14,6 3):recon-all.log:see attached hope for your reply!

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mideface: facemask not found
by Aaron Tanenbaum 10 Aug '24

10 Aug '24

External Email - Use Caution I have been writing scripts with the mideface program. Her the exact line of code i am using. mideface --i $Anatfolder/${mprs[0]}_T1w.nii.gz --odir $defacefolder --o $defacefolder/bids/${mprs[0]}_desc-defaced_T1w.nii.gz --pics --facemask facemask.mgz I am using FreeSurfer 7.4 on Ubuntu 20.04 and 22.04 I noticed that it will not honor the --facemask flag. I found the exact issue is on line 310 of where it set the facemask variable. I am fine with the standard name, I was just following instructions on one of your tutorial. I just want to point this out.

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Re: [Freesurfer] Hypothalamic region segmentation
by fsbuild 09 Aug '24

09 Aug '24

External Email - Use Caution  Hello Raphaela, You probably installed the Intel Mac binaries to run on your Silicon Mac with an M1, M2, or M3 arm64 chip.  But not all Intel code will run on the newer arm64 Macs.   You instead need to download and install the Silicon Mac nightly freesurfer build. To remove your current freesurfer install, you can try running the uninstall script from the command line under what you set FREESURFER_HOME to, $ cd $FREESURFER_HOME$ sudo bash uninstall.sh Once you have removed your current freesurfer installation, you can download and try installing the development build arm64 pkg, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesu… Right click with the mouse on the .pkg file and select “Open with —> install.app (default)".  Then follow the prompts in the installer windows. You should be using the python distribution included in the Freesurfer distribution under $FREESURFER_HOME/python.  The mri* commands that need python should automatically run it when those commands are issued on the command line, in a script, etc.  You can also run it directly from the command line as “fspython” after you set FREESURFER_HOME and source the setup file for the shell you run in the terminal window, e.g., $ export FREESURFER_HOME=/Applications/freesurfer/dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted …$ which fspythonfspython The freesurfer python (fspython) is python 3.8 and should include the necessary packages including a tensorflow package.  If you use a different python, e.g., 3.11, with different package versions installed, etc.., then commands may not run or work correctly. - R. On Aug 9, 2024, at 15:39, Raphaela C <freepoemi(a)gmail.com> wrote:        External Email - Use Caution        Dear the Freesurfer community, I am trying to segment the sub-ROIs of the hypothalamus using the mri_segment_hypothalamic_subunits tool, but I keep getting an error that says "zsh: illegal hardware instruction." I ran the recon-all command first and then this segmentation command. The first time I tried to run this command, it didn't prompt me to install tensorflow, so I manually installed it, but I'm still getting this error.  I am using a Mac OS Sonoma 14.1, python 3.11.6, and tensorflow  Would appreciate any advice. Thanks!_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hypothalamic region segmentation
by Raphaela C 09 Aug '24

09 Aug '24

External Email - Use Caution Dear the Freesurfer community, I am trying to segment the sub-ROIs of the hypothalamus using the mri_segment_hypothalamic_subunits tool, but I keep getting an error that says "zsh: illegal hardware instruction." I ran the recon-all command first and then this segmentation command. The first time I tried to run this command, it didn't prompt me to install tensorflow, so I manually installed it, but I'm still getting this error. I am using a Mac OS Sonoma 14.1, python 3.11.6, and tensorflow Would appreciate any advice. Thanks!

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Inconsistency between mean cluster cortical thickness value and lme_lowessPlot
by Dan Levitas 09 Aug '24

09 Aug '24

External Email - Use Caution I've been performing a LME longitudinal analysis on a dataset with two groups (controls, clinicals), where each participant completed two MRI scans (pre, post). I was examining a particular surface cluster that arose from a time*group interaction effect. I used the *--olab* option from the *mri_surfcluster* function to determine the vertex IDs from the particular cluster, and used the following code to determine the cluster means of (control_pre, clinical_pre, control_post, clinical_post) from the cluster: *[Y,mri] = fs_read_Y(lh.thickness_sm15.mgh'); % get surface data* *Qdec = fReadQdec(sprintf('%s/long.qdec.table.dat', qdec_table_path));Qdec = rmQdecCol(Qdec,1); % (removes first column)sID = Qdec(2:end,1); % (grabs the subjects' IDs)Qdec = rmQdecCol(Qdec,1); % (removes the subjects' Is ID column)M = Qdec2num(Qdec); % (converts to a numeric matrix)[M,Y,ni] = sortData(M,1,Y,sID); % (sorts the data)time = M(:,1);group = M(:,4);* *label_file = 'lh_cluster_vertices-0001.label' % from mri_surfcluster output* *dataStruct = importdata(sprintf('%s/%s', label_file.folder, label_file.name <http://label_file.name>));vertices = dataStruct.data(2:5:end); % select the rows containing the surface vertex IDscluster_data = Y(:, vertices);control_pre = cluster_data(group == 0 & time == 0, :);clinical_pre = cluster_data(group == 1 & time == 0, :);control_post = cluster_data(group == 0 & time > 0, :);clinical_post = cluster_data(group == 1 & time > 0, :);* From this code I get the following averages for each designation: 2.4397, 2.4340, 2.4069, and 2.4423. When, however, I plot the data with* lme_lowessPlot(time ,cluster_data, 0.70, group)*, the values are dissimilar from what I calculate. The LME documentation warns that "lowess plots can also be misleading, as it plots averages that could be affected by dropout etc", but I'm unsure what that means here, as the data has already been processed. I'm curious what the reason is for this inconsistency. Thank you. Dan

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making the face mask thicker mideface
by Aaron Tanenbaum 09 Aug '24

09 Aug '24

External Email - Use Caution Is there a way to make the face mask generated by mideface thicker? On its own it is fine however when we need to deface a T2 there may be some motion such that the mask does not do well when registered to the T2.

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run_samseg: Optimizer: maximalDeformation is too small; stopping; killed
by Ringki Marie Siewert 08 Aug '24

08 Aug '24

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Re: [Freesurfer] Older tksurfer and tkmedit (FS version 5.0.0) fail to launch: glut issue?
by fsbuild 07 Aug '24

07 Aug '24

External Email - Use Caution  For something released on CentOS4 like the 5.0.0 release mentioned in your email, you are probably better off running CentOS4 in a VM or container which in turn is hosted on a machine running a current/supported version of Linux, e.g., Rocky8, Rocky 9, Ubuntu 22, Ubuntu 24, etc.   That is the usual way to preserve such an old OS environment.  The version of OpenGL or system libraries something was built against on CentOS4 back in 2011 are not expected to be backwards compatible or run on a current system with an OS some 3+ revisions newer. There are virtualbox disk image archives for Freesurfer 5.0.0 (*.vdi) files underhttps://surfer.nmr.mgh.harvard..edu/pub/dist/freesurfer/5.0.0/The complete 7.5G .vdi file is,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.0.0/freesurfer-… you have root/admin privileges to install VirtualBox on some machine, then you should be able to import that .vdi file into VirtualBox  - which is likely a CentOS4 VM.  I believe Freesurfer 5.0.0 will already be installed there.  You could also try running the VirtualBox application on a Mac or Windows machine. - R. On Aug 7, 2024, at 19:19, Raij, Tommi A. <RAIJ(a)mgh.harvard.edu> wrote:Dear Surfers, I am trying to launch tksurfer/tkmedit in the stable 5_0_0 environment in the Martinos network, but this fails with glut segmentation errors. FS version 6 tksurfer works on the same machine and data, but I need to create some figures that match version 5. We already tried with a different user and a few years older linux box, same issues. Any suggestions would be greatly appreciated! For example, is there a variable that we could set to point to an older OpenGL version? (My LD_LIBRARY_PATH has not been set, and my PATH does not include anything pointing to /usr/lib or /usr/lib64) Details: on machine rukki (locally at terminal): setenv USE_STABLE_5_0_0source /usr/local/freesurfer/nmr-stable50-envcd $MY_SUBJECTS_DIR Checking version:freesurfer...You are running this version of FreeSurfer:  freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 echo $FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 cp -r $FREESURFER_HOME/subjects/fsaverage $MY_SUBJECTS_DIR/.chmod -R 777 fsaverage [rukki:sphsm10-ffx] (nmr-stable5.0-env) tksurfer fsaverage lh inflated subject is fsaveragehemi    is lhsurface is inflatedsurfer: current subjects dir: <$MY_SUBJECTS_DIR>surfer: not in "scripts" dir ==> using cwd for session rootsurfer: session root data dir ($session) set to:surfer:     <$MY_SUBJECTS_DIR>Reading image info <$MY_SUBJECTS_DIR>/fsaverage)Reading <$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgzsurfer: Reading header info from /<$MY_SUBJECTS_DIR>/fsaverage/mri/orig.mgz[rukki:sphsm10-ffx] (nmr-stable5.0-env) .... after which there is no screen output. The file xdebug_tksurfer was generated: [rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tksurfer SegfaultInitializing glutxDebug stack (length: 1)  00:   00: Initializing glut SegfaultInitializing glut[rukki:sphsm10-ffx] (nmr-stable5.0-env) [rukki:sphsm10-ffx] (nmr-stable5.0-env) echo $DISPLAY:3 setenv DISPLAY :0 does not fix the issue (results in GLUT: Fatal Error in tksurfer.bin: could not open display: 0) I also tried fsaverage4, fsaverage5, fsaverage6, and bert, copied from the same folder into my $SUBJECTS_DIR, same result. The issue is not specific to tksurfer: tkmedit -f fsaverage/mri/T1.mgz ===================================ERROR: A segfault has occurred. This is not your fault,  : but is most likely an unrecoverable error and has  : made the program unstable.  :  : Please send the contents of the file .xdebug_tkmedit  : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu  :  : Now exiting...  :[rukki:sphsm10-ffx] (nmr-stable5.0-env) more .xdebug_tkmedittkmedit started: Wed Aug  7 16:54:21 2024 tkmedit.bin -f fsaverage/mri/T1.mgz  $Id: tkmedit.c,v 1.341..2.1 2010/08/04 20:47:28 greve Exp $ $Name: stable5_0_0 $Set user home dir to ($MY_SUBJECTS_DIR)Set subject home dir to fsaverage/mri/T1.mgz SegfaultImporting volume with MRIreadxDebug stack (length: 5)          04: Volm_ImportData( this=0x3447db0, isSource=./fsaverage/mri/T1.mgz )          04: Importing volume with MRIread        03: LoadVolume( iType=0, isName=fsaverage/mri/T1.mgz, ibConform = 0 )        03: Reading data into volume      02: ParseCmdLineArgs( argc=3, argv=tkmedit.bin )      02: Loading volume fsaverage/mri/T1.mgz    01: main()    01: Parsing command line arguments  00:   00: [rukki:sphsm10-ffx] (nmr-stable5.0-env) My OpenGL version:[rukki:sphsm10-ffx] (nmr-stable5.0-env) glxinfo | grep "OpenGL version" OpenGL version string: 4.6.0 NVIDIA 550.54.14The other machine we tried had OpenGL version 4.6.0 NVIDIA 535.54.03 Thank you! Best regards, Tommi --- Tommi Raij, MD, PhDDirector, TMS Clinical Research MGH/MIT Athinoula A. Martinos Center for Biomedical ImagingBldg 149, 13th stCharlestown, MA 02129 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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