Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30059 discussions

Re: [Freesurfer] Support Request NextBrain
by fsbuild 28 Feb '24

28 Feb '24

External Email - Use Caution  The mri_synthseg script and python in the freesurfer disrtibution you are running are not entirely compatible with the arm64 M1, M2, M3 processors in silicon Macs.   You could try installing and running the development build of Freesurfer for the silicon Mac via the link below.  (After download, right click on the .pkg installer, and select open with default, then follow the prompts). https://secure-web.cisco.com/1lATTVPHpR_oCFmftTB7zqKpLVwajHCxZOKmxSn1tiCG2Y… We would be interested to know if you run into such issues with the above development build.  Please keep in mind a development build can be unstable and has not been tested like an actual release.  Your numerical result may differ with the development build compared to the previous build/release. - R. On Feb 28, 2024, at 14:25, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote:Dear Support Team,I'm reaching out for assistance with setting up NextBrain - mri_synthseg. Unfortunately, I could not make it work. There seems to be an issue with the np.float128-section. This error keeps showing up: <image.png>I have also tried to delete np.float128 from the script (as per suggestion from my colleague). However, the same error showed up. I'm working on a macOS M1. I would be very grateful for your assistance. Best, Helen ______________________ Helen Friedrich, B.Sc.Doctoral Student Netstim Laboratory Center for Brain Circuit TherapeuticsDepartment of Neurology Harvard Medical SchoolBrigham and Women’s Hospital 75 Francis St, Boston MA 02115 brighamandwomens.org   <Outlook-jaw0jfh4.png> _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Support Request NextBrain
by Friedrich, Helen 28 Feb '24

28 Feb '24

Dear Support Team, I'm reaching out for assistance with setting up NextBrain - mri_synthseg. Unfortunately, I could not make it work. There seems to be an issue with the np.float128-section. This error keeps showing up: [cid:a803f68d-8b94-414b-b0c6-f99cb634bf99] I have also tried to delete np.float128 from the script (as per suggestion from my colleague). However, the same error showed up. I'm working on a macOS M1. I would be very grateful for your assistance. Best, Helen ______________________ Helen Friedrich, B.Sc. Doctoral Student Netstim Laboratory Center for Brain Circuit Therapeutics Department of Neurology Harvard Medical School Brigham and Women’s Hospital 75 Francis St, Boston MA 02115 brighamandwomens.org [cid:923a5881-c8ab-405a-b7c5-25e55a108acc]

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Conference: Thalamocortical networks, May 16-17 San Sebastian, Spain
by 刘梦醒 28 Feb '24

28 Feb '24

External Email - Use Caution We are pleased to announce "*Thalamocortical networks (ThalNet): Bringing together cellular and cognitive neuroscience*", which will take place in person this *May 16-17 *at the Miramar Palace in *Donostia–San Sebastián*: https://secure-web.cisco.com/1OS0_akv0X2OFqkClRNexoTXkrzp2IxsLrRHYZLD531M4n… To understand thalamic function and structure represents a formidable neuroscientific challenge, wherein the collaboration between cellular and cognitive neuroscientific approaches holds much promise. Recognizing the potential synergy between these two disciplines, ThalNet is aimed at convening world experts from both realms and at setting the bases to initiate, foster, and develop interactions among researchers from these fields to further advance and strength our understanding of thalamocortical and corticothalamic networks. We look forward to welcoming you to Donostia-San Sebastián and to this exciting scientific event, which includes world renowned speakers on the topic. ThalNet scientific, organizing and administration committees https://secure-web.cisco.com/1OS0_akv0X2OFqkClRNexoTXkrzp2IxsLrRHYZLD531M4n… -------------- Liu Mengxing Postdoc, Tufts University

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Too large volumes thalamus segmentation in version 7.2
by Katharina von Kriegstein 27 Feb '24

27 Feb '24

Dear List, We are using the thalamic segmentation and have encountered too large nuclei volumes. We are aware of the bug in previous Freesurfer versions reported here https://secure-web.cisco.com/1IbBjsoyLKSxbo51anCmnlGJ7AZlAHQC-iMHoutsQKt5em… . In version 7.2 this bug is fixed. Does someone else have similar difficulties with too large volumes? For example, our LGN is 259 mm3 (left) and 304 mm3 (right), while in the original paper for the thalamus segmentation (Iglesias et al. 2018), it is 124 mm3, which is close to the size reported by histological studies. Thanks for reading! Katharina _ _ Katharina von Kriegstein Professor of Cognitive and Clinical Neuroscience Vice-Dean Faculty of Psychology TUD Dresden University of Technology Chemnitzer Str. 48b, 01187 Dresden Phone +49 (0) 351-463-43145 https://secure-web.cisco.com/1gJ3pcdCtydEP4JcYC_B04s_xcYKuSS0r7VoHh7Z0azmyO… https://secure-web.cisco.com/12zaO7jd5zPchZlNamn2OOwsicMw7Cg6FNxaL13gnPuKZw… External Email - Use Caution

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recon all with optiBET brain mask
by BALBONI Irene 27 Feb '24

27 Feb '24

External Email - Use Caution Hello, I would like to run recon all on a batch of subjects using 2 inputs (mprage and mp2rage). I would also like to run recon all using as brain mask not the standard brain mask generated by recon-all itself but a previously created optiBET. Would you have any suggestion on how to proceed? I tried simply replacing the brainmask file with the optiBET but it did not work. Just for context all my participants (150) have been already segmented using recon-all but we noticed during quality control that we still have skull stripping and pial surface errors for the majority of them and that is why we would like to implement the optiBET mask. Thanks for your help, Irene Balboni PhD student She/Her Institute de plurilinguisme<https://secure-web.cisco.com/1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duH…> | Université de Fribourg & Brain and Language Lab<http://secure-web.cisco.com/1GVUYNYViIIVEm2bvje-SiFox0WAIrWlf7gC0y8Dy1Yk6xj…> | Université de Genève c/o Campus Biotech Chemin des Mines 9 – 1202 Université de Genève, CH +41(0)223790141 Twitter<https://secure-web.cisco.com/17WKW8eFYGf6kC7ikhhz87_g3_OExqqtlPMTRdUfjaGR0u…> | ResearchGate<https://secure-web.cisco.com/17QR3OuPCdu6j4aAtW1iy0qnt2WV8MA0yHG3gonUNgbpno…> | Linkedin<https://secure-web.cisco.com/10d7bSA4mUh4az6x-hBwYc5c1373f-jWI1YMV5SjB-YHxE…>

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Updated instructions for running Freesurfer in a Linux VM (virtual machine)
by fsbuild 26 Feb '24

26 Feb '24

External Email - Use Caution  Instructions about how to setup a VM running Ubuntu 22.04 LTS Linux have been updated on the wiki page,  https://secure-web.cisco.com/1-hfMzPT3UMB77kyvVjV7UDTVoojwvFmLCgo5iFkfwXwZ25LXFS9Roz8W9yuwq3ZMgs5tjQSEKQlcqIQbRxJ1rps2AabjEIivAzU8ekg5AsJLT6mntG2Nc4NnzZYDPJZG2wf_aLnz6uKLNaustProbSHYKiMbskeae7cLki3u_nSnw4xu4chaYhm-Z5kLiuCwcqECsDkdCMoITT-JKqqCHPkmz-brMCz3F9oCcmaqFMirOwqvqcbah9n7ycsFnHd3RDgkGDoMo6zuiX8aecB8B0MO5X6QvJKUslOgGjkBUQ4W4ItrfjjElVnPeg2YV9CgmgVdxPZUx-arGQMnQ7ZyPg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67The instructions include how to install and run the current Freesurfer release (7.4.1 from June 2023). Please keep in mind that while the VirtualBox virtualization application runs on hosts with Intel processors, it does not run on arm64 machines (including silicon Macs with M1, M2, M3 chips). - R.

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Segmentation White matter bad
by lejia2011411409 26 Feb '24

26 Feb '24

External Email - Use Caution Dear freesurfer experts, A large amount of subjects got segmentation white matter bad (some dark white matter cannot be recognition below 57 slices). Attachment show this problem. I used 'kvlEMSegment brainmask.mgz 3 4 4 ' to segment white matter again. while there reported kvlEMSegment: command not found. Do you have any solutions for this? Thanks in advance. Best wishes, Lejia

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Re: [Freesurfer] Permission denied error from -localGI
by Douglas N. Greve 26 Feb '24

26 Feb '24

That is weird -- ft_read_mri is not one of our files. Can you send the command line and the *full* terminal output? The lGI stuff is pretty old and does not have a maintainer. On 2/26/2024 1:40 PM, Michael Ruvalcaba wrote: > > External Email - Use Caution > > Hi Douglas, > > Yes I can definitely do that! > > After I run the recon -all part for a specific subject using > freesurfer 7.2.0 in MATALB, I then run the below code: > > %% 4c. Load Freesurfer Pre-Op MRI (do not edit) > addpath('/usr/local/freesurfer_x86_64-7.2.0/matlab'); > fsmri_pre_acpc = ft_read_mri([subdir > '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); > > Which gives me the following error: > > /bin/bash: > /scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh: > Permission denied > > ERROR: could not open > /scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh for reading > ERROR: loading > /home/knight/ecog/DATA_FOLDER/UCSD/SD11/3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz > as MGH > Dot indexing is not supported for variables of this type. > > Error in ft_read_mri (line 401) > ndims = numel(size(tmp.vol)); > > Error in SD11_Recon_Pipeline (line 197) > fsmri_pre_acpc = ft_read_mri([subdir > '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']); > > > I don't get this error when using freesurfer 6.0.0 and using those > above commands. So I'm guessing it's because freesurfer 7.2.0 is > trying to write something to a scratch file that doesn't even exist? > > Thank you for your help! > > Best, > Michael Ruvalcaba > Knight Lab > Helen Wills Neuroscience Institute > University of California, Berkeley > > > On Fri, Feb 23, 2024 at 10:26 AM Douglas N. Greve > <dgreve(a)mgh.harvard.edu> wrote: > > Can you send more info? Eg, command line, all terminal output, > version of FS you are using? > > On 2/6/2024 6:18 PM, Michael Ruvalcaba wrote: >> >> External Email - Use Caution >> >> Hello, >> >> I had a similar question you had in the past thread >> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72609.html >> <https://secure-web.cisco.com/1zJkMv9aRmMM6PokM8jDCRUGLybtdGCgeH3ZTgzjLrgSV_…>) >> but I cannot seem to access the link where you solved this issue. >> It looks like Tashrif helped you and he informed me to ask you >> >> Can you help me with this by chance? I tried opening an account >> and logging in but it says my account hasn't been approved yet :( >> and I'm not sure who to contact to get it approved. It's been >> months. >> >> Thank you! >> >> Best, >> Michael Ruvalcaba > > The information in this e-mail is intended only for the person to > whom it is addressed. If you believe this e-mail was sent to you > in error and the e-mail contains patient information, please > contact the Mass General Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline > <https://secure-web.cisco.com/1NtHoQ5l2JOZE9k3SI7BCp1fNSP7MoxRtpOqh63C_iPwsC…> > . > > > Please note that this e-mail is not secure (encrypted). If you do > not wish to continue communication over unencrypted e-mail, please > notify the sender of this message immediately. Continuing to send > or respond to e-mail after receiving this message means you > understand and accept this risk and wish to continue to > communicate over unencrypted e-mail. >

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if: Expression Syntax - preproc-sess
by Stefano Delli Pizzi 26 Feb '24

26 Feb '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run preproc-sess with -nomc option preproc-sess -s subj -surface fsaverage lhrh -fwhm 0 -nomc -mni305 -fsd rest -per-run -sliceorder up -force if: Expression Syntax. This error occurred before to create the file with slice timing correction The error did not occur when I run the preproc-sess command line without the -nomc option. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Platform: Darwin Kernel Version 21.6.0

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Re: [Freesurfer] Freesurfer white matter overestimated
by Douglas N. Greve 26 Feb '24

26 Feb '24

It looks like the volume has very poor contrast. What volume are you displaying it on? Can you take a pic on the nu.mgz? On 2/26/2024 2:53 AM, Luisa Klahn wrote: > > External Email - Use Caution > > Dear Douglas, > Please find attached the pictures for the following issue: > I am processing structural data from a 3T scanner using Freesurfer > version 7.3.2. For some subjects, the grey matter looks very thin, and > the white matter looks overestimated. I'll attach screenshots of the > brainmask, wm mask, and T1 including wm and pial surface lines. > I have tried to set control points into the wm but this did not change > the results. > Does anyone have an idea? Would it be possible to change the intensity > settings in the recon-all command? > > Thanks for helping! > Best, > Luisa

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