Freesurfer August 2023

freesurfer@nmr.mgh.harvard.edu

89 participants
126 discussions

Start a nNew thread

mailing list
by Pavlina.Pokosova＠fnmotol.cz 17 Aug '23

17 Aug '23

1 0

Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS
by fsbuild 16 Aug '23

16 Aug '23

External Email - Use Caution  Since that did not work, I suggest you try some of the other suggestions in that posting about changing the permissions on files related to _apt..  If you are not a system administrator, then perhaps one could help you out.  It reads to me like different fixes worked for various people depending upon their system.  You could check to see if there are any Ubuntu system updates available as that might help, but I don’t see any reports of that providing a fix.  I would expect what you list to happen with any binary RPM you download and try to install, i.e., I don’t see this as an issue with the freesurfer installer. - R. On Aug 16, 2023, at 06:19, Praise Matsekete <MTSPRA001(a)myuct.ac.za> wrote:        External Email - Use Caution        Good day,Kindly find attached a screenshot of what I tried to do in the terminal as well.Kind regards,Praise From: Praise Matsekete <MTSPRA001@myuct.ac.za>Sent: Wednesday, 16 August 2023 12:08To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS Good day,Thank you so much for the help. I tried to "chmod 777" the .deb file before  installing it. However, I am still experiencing the same issue.Kindly find attached a copy of the text from the terminal after I tried this.Kind regards,Praise MatseketeFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of fsbuild <fsbuild@contbay.com>Sent: Tuesday, 15 August 2023 21:48To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Cc: Praise Matsekete <MTSPRA001@myuct.ac.za>Subject: Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS CAUTION: This email originated outside the UCT network. Do not click any links or open attachments unless you know and trust the source.        External Email - Use Caution        Hello Praise,This post,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://askubuntu.com/questions/908800/what-does-this-apt-error-message-d… indicates it is from a permission problem with _apt on the system (which may have been an Ubuntu bug/issue).    One of the more innocuous fixes suggested there is to down protect or “chmod 777” the .deb package and then try to install it.  Other fixes involve changing the permissions of system files.  I have not seen that error testing the install in a newly made Ubuntu 22 docker container.- R.On Aug 15, 2023, at 10:43, Praise Matsekete <MTSPRA001(a)myuct.ac.za> wrote: Download is performed unsandboxed as rootDisclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://secure-web.cisco.com/1n1CU5pgJva0i88ZdZvGUVVJvFn05Or9gojbkdZVXUZHyo4… or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://secure-web.cisco.com/1ZM9iFYqL-twUClMROcbvwPaSPzsAlYMRElsr6iQpdf2UI… from 2023-08-16 12-04-10.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Password for unzipping virtual machine image
by Jochen Ditterich 16 Aug '23

16 Aug '23

External Email - Use Caution Hi, Could you please send me the password for unzipping the Freesurfer virtual machine image? Thank you and best regards, Jochen Ditterich --------------------------------------------------- Jochen Ditterich, Ph.D. Professor Center for Neuroscience Dept. of Neurobiology, Physiology & Behavior Co-Director, Center for Neuroengineering & Medicine University of California 1544 Newton Court Davis, CA 95618 USA office: +1 (530) 754-5084 lab: +1 (530) 754-6987 fax: +1 (530) 757-8827

1 0

Re: [Freesurfer] Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS
by fsbuild 16 Aug '23

16 Aug '23

External Email - Use Caution Hello Praise, This post, https://secure-web.cisco.com/13ufO8OPW7q_Ihf7Z4dQTf5tWtAWOGypFw1c5438ElaNLx… - indicates it is from a permission problem with _apt on the system (which may have been an Ubuntu bug/issue).    One of the more innocuous fixes suggested there is to down protect or “chmod 777” the .deb package and then try to install it.  Other fixes involve changing the permissions of system files.  I have not seen that error testing the install in a newly made Ubuntu 22 docker container. - R. On Aug 15, 2023, at 10:43, Praise Matsekete <MTSPRA001(a)myuct.ac.za> wrote: Download is performed unsandboxed as root

2 2

recon-all error
by Rosalia Dacosta Aguayo 16 Aug '23

16 Aug '23

External Email - Use Caution Dear Freesurfer team, I got the following error message after running recon-all -autorecon-pial -subjid sub-073_ses-BSL SUBJECT sub-073_ses-BSL DATE Wed 16 Aug 10:35:09 CEST 2023 USER rosalia HOST rosalia-Lenovo-Y520-15IKBN PROCESSOR x86_64 OS Linux Linux rosalia-Lenovo-Y520-15IKBN 5.19.0-45-generic #46~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 7 15:06:04 UTC 20 x86_64 x86_64 x86_64 GNU/Linux 7.3.1 (freesurfer-linux-ubuntu20_x86_64-7.3.1-20220723-115e466) /home/rosalia/software/freesurfer/bin/recon-all PWD /home/rosalia/Desktop/CAN_RUTI/sub-073_ses-BSL/mri CMD mri_brainvol_stats sub-073_ses-BSL I attach the recon-all.log file for inspection. It seems the problem is with: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 i was having troubles with the skull-stripping of this subject and what I did, and other times worked for me just fine, is run fsl_anat to skull-strip the image and then: mri_convert T1_biascorr_brain.nii.gz brainmask.mgz I replaced the problematic brainmask for this new one and ran the command above. It seems it has problems running it without troubles. Before this, I tried watershed modifying it with different "h" and also gcut and nothing seemed to work improving the skull stripping. I wonder if you could help me with this one subject. Thank you in advance for all your help. Kind regards, Rosie

1 0

3D printing from freesurfer
by Pukovisa Prawiroharjo 15 Aug '23

15 Aug '23

External Email - Use Caution can we print the aseg and aparc image in fresurfer to 3D model for print it in 3D printer? best regards *Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD* Neurobehavior Consultant, Neurology Specialist Neurology Department, Faculty of Medicine, Universitas Indonesia Chair of Bioethics Cluster IMERI UI Chair of International Policy Div, Board of Development Med Services IDI <https://secure-web.cisco.com/1dMsDqGkx9bbbXk-SMdyeEGdwcNvhizuvbawstRRu2NMPt…> Bebas virus.http://secure-web.cisco.com/1eqbIQxRatvR4jpMztRO8nqYpwhONsgWSEt3RaxfS… <https://secure-web.cisco.com/1dMsDqGkx9bbbXk-SMdyeEGdwcNvhizuvbawstRRu2NMPt…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

Trouble installing Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS
by Praise Matsekete 15 Aug '23

15 Aug '23

External Email - Use Caution Good day, I hope you're well. I am experiencing difficulty installing the latest version of Freesurfer 7.4.1 on Ubuntu 22.04.2 LTS. I downloaded the following .deb file from the Freesurfer webpage: freesurfer_ubuntu22-7.4.1_amd64.deb After downloading the file and navigating to the directory I stored it in, I tried to install it by running the following line in the terminal: $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb Unfortunately, I keep getting an error that reads: "N: Download is performed unsandboxed as root as file 'home/user/Documents/Praise/freesurfer_ubuntu22-7.4.1_amd64.deb' couldn't be accessed by user '_apt'. - pkgAcquire: : Run (13:Permission denied)" I am unsure what the problem is and would appreciate some help. Thank you so much for your time and assistance. I look forward to hearing from you. Kind regards, Praise Matsekete Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://secure-web.cisco.com/1knZJeohbnbV4U3PoD30TvfKOHoGhLBW5ttR3S-lD8019gl… or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://secure-web.cisco.com/1hOzg9gGzkaTfDzmc7K9r9agau6LiaB730Iv1HGCAoCVO6…

1 0

can we make 3D printing from freesurfer
by Magang Visa 15 Aug '23

15 Aug '23

External Email - Use Caution can we print the aseg and aparc image in fresurfer to 3D model for print it in 3D printer? thanks omi, Faculty of Medicine Universitas Indonesia <https://secure-web.cisco.com/1fP-sLwZnuIaXHmZECvtuLLwY-ogC93axbNcAu_xaYFfwS…> Bebas virus.http://secure-web.cisco.com/1sSVC0cZe6B7-vXLkmfiMkwC8YKgYYMJsKfppCZ54… <https://secure-web.cisco.com/1fP-sLwZnuIaXHmZECvtuLLwY-ogC93axbNcAu_xaYFfwS…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

mris_find_flat_regions help
by Alastair Snell 15 Aug '23

15 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to locate flat regions along the pial surface of an MRI scan, ideally about 5mm in size. I am using mris_find_flat_regions in order to do this. Unfortunately, the information page (https://secure-web.cisco.com/1NI_7_9GXEGWvnwy1GzFMB4NGJEbyzBihtm4Wzlv7x59Qo…) isn't informative enough for me to solve my issue. I have used the command on lh.pial in the good_output folder located in buckner_data of the tutorial data set. This returned lh.pial.flat.w. I used mris.convert to convert this into lh.pial.flat.asc - which is a series of vertex numbers on the left column and a column of 1's on the right. I want to be able to visualize these regions in freeview (tksurfer does not work at my institution), cluster them into local groups (patches) of vertices, and export one of these clusters/patches as a set of co-ordinate vertices. I've searched the list and no similar issues have been reported. Does anyone have any thoughts on how to achieve this? 1) FreeSurfer version: freesurfer 7.3.2 (linux) 2) Platform: Linux Ubuntu 22.04 3) uname -a: Linux wks6 5.19.0-46-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jun 21 15:35:31 UTC 2 x86_64 x86_64 x86_64 GNU/Linux Many thanks in advance, Alastair Snell

2 1

Laminar fMRI course at MGH in Boston, MA, Oct. 2-5, 2023
by Polimeni, Jonathan,PHD 14 Aug '23

14 Aug '23

External Email - Use Caution We are pleased to announce our upcoming four-day educational course in Laminar fMRI. This course will provide an introduction to fMRI of cerebral cortical layers, and will provide didactic lectures spanning neuroscientific background, high-resolution fMRI data acquisition and analysis, interpretation, and publication, focused on the practicalities of conducting a successful experiment, as well as hands-on training in data analysis. It is designed for beginners who are new to laminar fMRI, however researchers at all experience levels are welcome! Where: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital (MGH), Boston, MA, USA. The course will be offered in-person, onsite at MGH, however there is a remote option available. When: October 2-5, 2023 Course Faculty: Peter Bandettini, Anna Blazejewska, Saskia Bollmann, Jingyuan Chen, Anna Devor, Jozien Goense, Daniel Gomez, Doug Greve, Faruk Gulban, Laurentius (Renzo) Huber, A. Tyler Morgan, David Norris*, Jonathan Polimeni, Robert Savoy, Kamil Uludag, Divya Varadarajan, Luca Vizioli (*: remote lecturer) Course Moderator: A. Tyler Morgan Course Organizers: Jonathan Polimeni, Anna Blazejewska, Laurentius (Renzo) Huber & Robert Savoy Course webpage, lecture topics, schedule, and registration: https://secure-web.cisco.com/18kCj7pWQk8Y5OmMA9_oqwuZ9c5ku_zXDpZ_87YZZJXGcP… Registration closes September 17; the number of attendees is limited. For more information: email us questions at laminarfmricourse(a)nmr.mgh.harvard.edu<mailto:laminarfmricourse@nmr.mgh.harvard.edu>

1 0

← Newer
1
...
4
5
6
7
8
9
10
...
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2023