Freesurfer

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Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)
by James Hengenius 29 Dec '23

29 Dec '23

External Email - Use Caution Hello FS experts, I downloaded some anatomical data. I have defaced full images and pre-skullstripped images for each participant. I tried the defaced images first, but FS skullstripping looks a little off (possibly because the defacing hides bits of the cranium in some images and causes problems in mri_watershed). So I would like to use the pre-skullstripped files as my initial inputs. I have placed the pre-skullstripped file for each participant in $SUBJECTS_DIR/$subjid/mri/orig/. Each participant's skullstripped input volume is named 001.mgz. I then submit the following command in a script to my slurm queue (after setting appropriate FS env vars), where the script input ${1} is the $subjid mentioned above: recon-all \ -subject ${1} \ -all \ -openmp 40 \ -noskullstrip The output log from FS ends with the following error. The function mri_em_register seems to be looking for brainmask.mgz, and fails to open it. If the input image is already extracted from the skull, do I need to manually call it brainmask.mgz rather than 001.mgz? Or am I missing something else in my function call (like order of flags)? Does -noskullstrip need to come before -openmp, for example? Thanks! Jim H. End of recon-all output: writing output to T1.mgz > 3D bias adjustment took 1 minutes and 20 seconds. > @#@FSTIME 2023:12:28:16:07:04 mri_normalize N 7 e 80.39 S 0.66 U 102.70 P > 128% M 581068 F 0 R 24411 W 0 c 32 w 229 I 0 O 0 L 1.00 1.38 9.22 > @#@FSLOADPOST 2023:12:28:16:08:25 mri_normalize N 7 1.99 1.66 8.64 > #------------------------------------- > #@# EM Registration Thu Dec 28 16:08:25 EST 2023 > /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri > mri_em_register -uns 3 -mask brainmask.mgz nu.mgz > /home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca > transforms/talairach.lta > setting unknown_nbr_spacing = 3 > using MR volume brainmask.mgz to mask input volume... > == Number of threads available to mri_em_register for OpenMP = 40 == > reading 1 input volumes... > logging results to talairach.log > reading > '/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca'... > GCAread took 0 minutes and 1 seconds. > average std = 7.2 using min determinant for regularization = 5.2 > 0 singular and 884 ill-conditioned covariance matrices regularized > reading 'nu.mgz'... > error: > > *mghRead(/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri/brainmask.mgz, > -1): could not open file^@error: mri_em_register: could not open mask > volume brainmask.mgz.^@* > @#@FSTIME 2023:12:28:16:08:25 mri_em_register N 7 e 1.42 S 0.25 U 1.43 P > 118% M 446804 F 0 R 108260 W 0 c 2 w 56 I 0 O 0 L 1.99 1.66 8.64 > @#@FSLOADPOST 2023:12:28:16:08:26 mri_em_register N 7 1.99 1.66 8.64 > Linux nia0918.scinet.local 3.10.0-1160.102.1.el7.x86_64 #1 SMP Tue Oct 17 > 15:42:21 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > recon-all -s 1000108_20252_2_0 exited with ERRORS at Thu Dec 28 16:08:26 > EST 2023 > For more details, see the log file > /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/scripts/recon-all.log > To report a problem, see > http://secure-web.cisco.com/1ywN1tDbl7MCg8OnWFYEA2Vcf-TaEWXJQlDYsrE7jJo4KqF…

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Brainstem segmentation without pre-processing
by Ganjizadeh, Ali, M.D. 28 Dec '23

28 Dec '23

External Email - Use Caution Good evening, I am trying to work with segmentBS.sh. I want to pass my .nii.gz files that are already pre-processed with HD-BET, but I don't want to use recon-all as the first step because it takes a lot of time. I also tried recon-all -autorecon2 and 3, but it resulted in an error. Is there any specific command that I will be able to pass my files directly to segmentBS.sh? Or is there any command for recon-all to only make subjects without processing or fast processing? Thank you, Ali Ali Ganjizadeh, M.D. (he/him) Postdoctoral Research Fellow Mayo AI Lab (Radiology Information Lab) Mayo Clinic-Rochester

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Help (Freeview fails to launch)
by Akira Kita 27 Dec '23

27 Dec '23

External Email - Use Caution I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz. Freeview fails to launch with the following error message: This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, How can I solve this? Akira

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Re: [Freesurfer] segmentBS.sh not found
by fsbuild 26 Dec '23

26 Dec '23

External Email - Use Caution  On linux, that file is under $FREESURFER_HOME/bin and will be found in your PATH after you setup the Freesurfer environment, e.g. for the 7.2.0 release installed via the .rpm file, you setup the environment with, $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0-1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.2.0-1 FSFAST_HOME       /usr/local/freesurfer/7.2.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.2.0-1/subjects MNI_DIR           /usr/local/freesurfer/7.2.0-1/mni $ which segmentBS.sh /usr/local/freesurfer/7.2.0-1/bin/segmentBS.sh $ segmentBS.sh -h      ERROR: cannot find Matlab 2014b runtime in location:      /usr/local/freesurfer/7.2.0-1/MCRv84… rest of output deleted .. So if you have not already installed the MATLAB runtime environment for the segmentBS.sh script, then you need to run the Matlab install script we provide.  For the Freesurfer install under /usr/local on linux, the Matlab install needs to be done with root/admin privileges which you can try via the sudo option, $ cd $FREESURFER_HOME/bin$ sudo  FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2014b … you will see output from downloading and installing the matlab runtime under /usr/local/freesurfer/7.2.0-1/MCRv84 …You should follow the instructions from the script output about how to set LD_LIBRARY_PATH, e.g., On the target computer, append the following to your LD_LIBRARY_PATH environment variable: /tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64: Your paths may be different, but you would modify the LD_LIBRARY_PATH setting as follows; I just cut and pasted the /tmp/* paths anover after "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:”, $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/tmp/tmp.e23XcWLTeV/install-target/v84/runtime/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/bin/glnxa64:/tmp/tmp.e23XcWLTeV/install-target/v84/sys/os/glnxa64 You could follow the same instructions as listed above for the 7.4.0 release, i.e.. change 7.2.0 to 7.4.0 in all the commands (and corresponding output should list 7.4.0 instead).  The segmentBS.sh in 7.4.0 might ask for a newer Matlab version like MCRv97.   In that case, the sudo command to run the fs_install_mcr script would be,$ sudo  FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b Once Matlab runtime is installed, try running segmentBS.sh again, $ segmentBS.sh -h  Directory of subject to process:    /usr/local/freesurfer/7.2.0-1/subjects/-h does not exist So change SUBJECTS_DIR to the path containing the subject data you want to process, $ export SUBJECTS_DIR=/path/to/my/subjects … then try running again ... - R. On Dec 26, 2023, at 19:32, Ganjizadeh, Ali, M.D. <Ganjizadeh.Ali(a)mayo.edu> wrote:segmentBS.sh

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segmentBS.sh not found
by Ganjizadeh, Ali, M.D. 26 Dec '23

26 Dec '23

External Email - Use Caution Greetings, I have tried FreeSurfer 7.4.1 and 7.2.0 for CentOS7. But neither of them has segmentBS.sh in the files. Could you help me to find the file? I want to pass T1 MRIs (in which the skull is removed already) and get brain stem segmentation only. Could you explain what the fastest command is to do this job? Thank you, Ali Ganjizadeh, M.D. (he/him) Postdoctoral Research Fellow Mayo AI Lab (Radiology Information Lab) Mayo Clinic-Rochester

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question regarding echo spacing and epi factor in TRACULA
by Hu, Bojia 22 Dec '23

22 Dec '23

Hello there, When we were trying the TRACULA tutorial, we noticed a discrepancy between the downloaded script and the wiki page. The echo spacing is set as 0.000689998 in the script, but it is exemplified in ms on the wiki page. For the epifactor, it is set as 139000.96811584961115829321 in the script, but on the wiki page it is 140. We are wondering which units we should be using for our dataset. Our protocol says that echo spacing is 0.55ms, and EPI factor is 116. Thank you for your help. Warm regards, Cynthia Hu

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SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields
by Heese, E. van (Eva) 22 Dec '23

22 Dec '23

External Email - Use Caution Dear FreeSurfer support team, I am running into some issues regarding the mandatory SUBJECTS_DIR writing permissions when running the hippocampal and amygdala subfields segmentation functionality<https://secure-web.cisco.com/1GxtLaQMhc8dCLk40Dqxx5gjSJCGqioQxX7dJnX4YO4XoD…> (segmentHA_T1.sh). I am using FreeSurfer 7.3.2 on a slurm server. We have a shared FreeSurfer installation which is the FREESURFER_HOME location for many users, hence the absence of writing permissions. When running the subfield segmentations, I get this error: mv: replace 'imageDump.mgz', overriding mode 0444 (r--r--r--)? Even when overriding this (by typing y), the error results into issues with the segmentations because it cannot access the imageDump.mgz file and thus cannot use it as the starting template for the segmentation. This has been suggested and confirmed by Philipp Saemann and Juan Eugenio Iglesias in separate correspondence. The short-term solution offered by our server admin was to make a local copy of the FreeSurfer installation (to be able to get writing permissions) and set the FREESURFER_HOME variable to this local copy. This seems a bit devious, considering many FreeSurfer users might face a similar issue on shared clusters without writing permissions. Is there another workaround possible? Thanks for your help. Best wishes, Eva van Heese ______________________________________________________ AmsterdamUMC disclaimer : http://secure-web.cisco.com/181PMcOVEvWHrKhQAbaRQ6z6TR591a4a86em9ZjTSVgyLTj…

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Killed procees during running WMH-SynthSeg
by 赵楚越 21 Dec '23

21 Dec '23

External Email - Use Caution Dear freesurfer experts, I have installed the develpment version of FreeSurfer on WSL with UNbuntu 20.04, when I try to run WMH-SynthSeg with mri_WMHsynthseg --i WMHsynthsegTset/ --o WMHsynthsegTset/ but the proceess seemed killed and nothing produced in the output directory. Would you recommend what I should change? Thank you so much! Following is the ouput in the commomand line window. Arguments seem correct; loading Python packages... Using cpu Using 1 thread(s) Preparing model and loading weights Working on image 1 of 1: WMHsynthsegTset/T1_1.nii Loading input volume and normalizing to [0,1] Upscaling to target resolution Pushing data through the CNN Killed Best, Chuyue

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Re: [Freesurfer] Freesurfer Digest, Vol 238, Issue 7
by Spapens, Jeltje (NP) 21 Dec '23

21 Dec '23

External Email - Use Caution Hi I have not received a response to my question yet I think __ On 13/12/2023, 08.53, "freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu>" <freesurfer-bounces(a)nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/13w96AyqB5Nk5Zlu_uq8_qAk6WErZ9a6rflAusUqF0Icp2… <https://secure-web.cisco.com/13w96AyqB5Nk5Zlu_uq8_qAk6WErZ9a6rflAusUqF0Icp2…> or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. FW: Boundary based registration (Spapens, Jeltje (NP)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 13 Dec 2023 07:48:55 +0000 From: "Spapens, Jeltje (NP)" <j.spapens(a)maastrichtuniversity.nl <mailto:j.spapens@maastrichtuniversity.nl>> Subject: [Freesurfer] FW: Boundary based registration To: "freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <802B8CE8-CF05-4066-809E-1B14866460CB(a)maastrichtuniversity.nl <mailto:802B8CE8-CF05-4066-809E-1B14866460CB@maastrichtuniversity.nl>> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Freesurfer developers, I want to register an MRI slap to a full FoV UNI scan of the same subject, but I get a false reorientation with my code (see attached image). I have tried multiple input and tried the script on different subjects. I also changed som flags such as -init-header and --cubic, but all seem to give the same results. bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --t2 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat ?trilin I would appreciate to hear your thoughts on this problem. Have a nice weekend and kind regards, Jeltje Spapens

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Re: [Freesurfer] Freesurfer/Freeview Version Compatibility
by fsbuild 20 Dec '23

20 Dec '23

External Email - Use Caution The freesurfer 6.X and 7.x release release notes summarize some changes for Freeview (listed below) since version 5 was released in 2013.   If none of the improvements in features/stability are relevant to what you are doing, then I don’t see why you could not revert to the older 5.X software.  But if you run into issues with a now ~10 year old version of Freeview, we may tell you to use the latest 7.4.1 release from June of 2023. - R. - - - - -  • New: interface for x virtual frame buffer (fsxvfb). When you run freeview from fsxvfb, no X server is needed. This is good for taking a bunch of pictures when you don't want freeview popping up all the time. Eg, fsxvfb freeview orig.mgz -ss mypic.png —quit • The filled.mgz can now be edited instead of the wm.mgz. The advantage to this is that filled.mgz is slightly further in the process and it is more intuitive. The filled.mgz is actually a segmentation of the subcortical mass. In Freeview, you can view it in outline mode, meaning that the edges of the segmentations are actually the surface that you are editing. After that, run recon-all with the -autorecon2-wm -autorecon3 options, just as you would if you had edited the wm.mgz..Landmark-based repositioning of surfaces. Did you ever want to just make the surface move through a certain point? You can do that now by creating point sets in freeview. Create a separate point set for each surface (lh, rh, white, and pial), then save it in subject/surf with a file name repos.$hemi.$surf.json where $hemi is either lh or rh and $surf is either white or pial. Then run recon-all with the -autorecon2-surfonly -autorecon3 options. Note that you can do this interactively inside of FreeView as well; look under Tools->Resposition Surface. If you do it interactively, the surface may be overwritten next time recon-all is re-run, but it gives you a chance to play with the repositioning.freeview - can now load and visualize diffusion orientation distribution function (ODF) data.FreeView changes: surfce path and label editing, surface annotation editing, automatic segmentation assisted by Geodesic Matting algorithm, displaying two time courses at the same time, better support for Mac (petsc error fixed on Mac) On Dec 20, 2023, at 14:07, Edwards, Vincent <Vincent.Edwards(a)utdallas.edu> wrote:        External Email - Use Caution        Hi, I'm following up on my quick question from this time last week. I have several brains that I sent through recon-all using Freesurfer 7. If I wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point edits, would I be able to do recon-all through Freesurfer 7?  Years ago, someone asked if they could do recon-all in an older version of Freesurfer and edit in a newer GUI. Doug said that was fine. My question is basically the inverse of their problem. I assumed that since Freeview is a GUI, the version used shouldn't have any actual impact on things as long as we returned to version 7 to recon-all. I just want to confirm that my assumption is correct?The pipeline would be: F7 (recon-all), F5 (edit with freeview), F7 (recon-all for pial/wm/cp's)Thanks,Vincent Edwards_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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