Freesurfer February 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
83 discussions

Creating a custom registration template with FreeSurfer template
by Asuka Toyofuku 29 Feb '24

29 Feb '24

External Email - Use Caution Dear Freesurfer experts, I have issues with creating a custom registration template. (I'm following this instruction: https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8… ) According to the instructions, we need to 1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate) 2) Register each subject to the new template (do for both lh and rh), resulting in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate 3) Get thickness values in the newtemplate space for GLM analysis 4) Create another average template based on the previous one: (Creates $SUBJECTS_DIR/newnewtemplate) I'm stuck with the 3) command. Instruction suggests: mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ... and this is my code: for d in Teen* do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness done ( I specified hemi and output because, without it, I got ERROR: no source hemi specified) My command led to an error saying: ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized So my questions are: a) what does it mean that "format for lh.surfreg.average_template.thickness not recognised"? Any ideas on how to fix this? b) Does this mris_preproc --surfreg command produce different smoothing mgh files? (e.g., fwhm10, fwhm15, fwhm20...?) Because standard mris_preproc before GLM analysis(https://secure-web.cisco.com/1lH2n5girv1pSO3WmL3I9nDeL07oFU0ViiAmz… are done with previously qcashed data (e.g., need thickness.fwhm10.fsaverage to run mris_preproc), but at this point, I don't have any of these thickness files with different smoothing levels. c ) If this mris_preproc --surfreg command does not generate a set of thickness maps in **newtemplate space** at different smoothing levels, what kind of command should I run? Any input is appreciated! Best regards, Asuka

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mri_synthseg fails with current model files (was Re: Support Request NextBrain)
by fsbuild 28 Feb '24

28 Feb '24

External Email - Use Caution I don’t believe the workaround will be supported or provided with future releases intended to run on Silicon Macs.  If there is still an issue with mri_synthseg running with the current model files in the freesurfer dev build, then please let us know the details. - R. On Feb 28, 2024, at 20:11, Sorby-Adams, Annabel <ASORBY-ADAMS(a)mgh.harvard.edu> wrote:Hi Helen,I managed to run mri_synthseg on my M2 Mac by coping over the model file to the 7.3.2 version of freesurfer, and installing the tensorflow workaround previously posted on the forum for apple silicon machines.I have not been able to get it to work on the 7.4 or most recent dev versions unfortunately. The work around for 7.3.2 isn’t ideal, but does the trick. Freesurfer gurus may have more insight though! AnnabelOn 28 Feb 2024, at 20:03, Friedrich, Helen <hfriedrich(a)bwh.harvard.edu> wrote:Hi R,Thanks for your quick response. We actually did that initially and it did not work unfortunately.Could you provide me with segmentations for a certain scan? Or do you see any other possibility to make it work? 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-rrf3zs4o.png> Von: fsbuild <fsbuild@contbay.com>Gesendet: Mittwoch, 28. Februar 2024 17:20An: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Friedrich, Helen <hfriedrich@bwh.harvard.edu>Betreff: Re: [Freesurfer] Support Request NextBrain         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/1lFsgk7vtXlatyZGhw2wfTf_WTyioo4BmLzbK… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be brighamandwomens.org   <Outlook-jaw0jfh4.png> _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1rwDcenDHH042rGVnR9ADpR-TvoThnsOLxqL-W… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<Outlook-rrf3zs4o.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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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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Freesurfer February 2024