Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Announcing FreeSurfer version 7.2
by Douglas N. Greve 23 Sep '21

23 Sep '21

We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug

4 5

How to get cortical volume from a particular atlas?
by DRON Noramon 23 Sep '21

23 Sep '21

External Email - Use Caution Dear Freesurfer Team I have a very naive question. I am in urgent need to get a cortical region volume base on the Harvard-Oxford Cortical Atlas(from FSL). I have T1 images in nifti files, brain extracted. How can I get the cortical volume using Freesurfer, and regions based on the Harvard-Oxford Cortical Atlas? Please, I am very new to Freesurfer and in the middle of installing Freesurfer to linux server. Can you tell me the steps or a link to your tutorial page? I am trying to find it on your wiki page and have trouble navigate around. Thank you in advance, Best regards Noramon The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

2 1

Migrating data from v6 to v7
by Amanda Boyes 23 Sep '21

23 Sep '21

External Email - Use Caution Hi fellow FreeSurfer users, I am part of a longitudinal project and have a large dataset that has been processed in v6. I have now upgraded to v7 and would like to update my processed data, retaining the existing manual masks and pial edits. I found an old ReconAllChanges page (January 27, 2006, last updated 2012) referring to this as a “legacy data set” https://secure-web.cisco.com/1MoVgZUSO9R-A8IjZAHqOzDT9Py5A4Mq4VNrsSGB5Dphed… I have also found a recon-all wiki page (https://secure-web.cisco.com/1EqY5oKya3ZRmkvhBV2hjYD2yCLyZAOJUT5Hd_RXPDPt5m… last updated 2017) suggesting the use of the following command for legacy datasets: recon-all -subject subjectname -all -legacy Unfortunately, the -legacy flag is not recognised in v7. I would be grateful for any advice on how to update my existing data from v6.0.0 to v7.2. Thank you in advance, Amanda Amanda Boyes My pronouns are she/her/hers PhD Candidate and Research Assistant (Youth Mental Health) Thompson Institute USC  Tel: +61 7 5456 3886 amanda.boyes(a)usc.edu.au | usc.edu.au<http://secure-web.cisco.com/1otQ0N4r7tGUgtK8BkwMQjmBlIsM1lQpsIY-owcgNEj3Pph…> [Logo, company name Description automatically generated] I acknowledge the Traditional Custodians of the lands and waters upon which the University’s campuses are located. I acknowledge their continuing connections to country and pay my respects to Elders past, present and emerging. University of the Sunshine Coast | CRICOS Provider Number: 01595D

2 2

Confusion about PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
by 周冬跃 23 Sep '21

23 Sep '21

External Email - Use Caution Dear FreeSurfer experts:I use the command recon-all qcache to get file sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.And I am confused that the cortical thickness in this file is measured in common space after sub is aligned with the common coordinate system or just measured in subject space after changing the vertex location in subject space?In other words, when a sub is aligned to the common coordinate system,the folding patterns changed.But I am not sure if the value of cortical thickness measures has been changed during this process?

2 1

QDEC command not found
by Fabiola Macruz 23 Sep '21

23 Sep '21

External Email - Use Caution Dear freesurfer experts, I have installed the freesurfer version 7.1.1 in my computer (Mac). After running the longitudinal pipeline in all the patients, I tried to open qdec for the analysis by typing qdec and the answer is "command not found". Could you help me, please? Many thanks, Dra. Fabíola Macruz MD from Faculdade de Ciências Médicas da Santa Casa de São Paulo PhD from Universidade de São Paulo Former Research Fellow from Stanford University Former Clinical Innovation Fellow/ Project Leader from Mass General Brigham Phone: + 1(650)686-0668 / + 55(11)99571-5906

2 1

Freesurfer version confusion
by Paul, Rahul 23 Sep '21

23 Sep '21

Hi freesurfer experts, I was using FreeSurfer v6 for my research. Recently, I started move to FreeSurfer v7.2. I encountered the following issue: Some patients, that had extra large error (xL error), were running fine (recon-all) in freesurfer 6 (it took time, but the process finished, and the segmentation was fine too) but in freesurfer 7, same patient recon-all encountered the extra large error (e.g., CORRECTING DEFECT 35 (vertices=9718, convex hull=1801, v0=40087 Command terminated by signal 11) and after couple of hours recon-all exited (recon-all -s 8375 exited with ERRORS ). I am not sure why recon-all is existing for freesurfer 7.2 and how can I stop that. Thank you Rahul

2 1

mri_glmfit 0 voxels in mask ERROR
by Tsiknia, Amaryllis 23 Sep '21

23 Sep '21

External Email - Use Caution Dear Freesurfer Team, I have been struggling with an error using the mri_gmfit command. I have been trying to run a simple surface-based group analysis on 28 subjects testing whether a continuous variable "OMEGA3_457" relates to various RSI measures while adjusting for the effects of gender. This is the error I am getting: [Image preview] and attached is my .fsgd file. The matrix file I am using is testing for the following contrast: 0 0 0.5 0.5. I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf command after using mri_concat to concatenate the RSI data for all 28 of our subjects into a single lh.N0s2_e4pos.00.mgh file. I have also attached the text file (containing all the paths to the subject data) that was fed into the mri_concat command. Any help would be immensely appreciated. Thank you, Amaryllis A. Tsiknia Imaging Researcher Department of Neurosciences University of California, San Diego atsiknia(a)health.ucsd.edu

2 3

Best graphics card for freesurfer?
by Falko Mecklenbrauck 23 Sep '21

23 Sep '21

External Email - Use Caution Hello Freesurfer Developers, the old Linux-Computer Freesurfer was running on broke down and now we need to buy a new one. The recommondations in the systems requirements were very helpful, but they seem a bit outdated. For Graphics Card it says: * /ATI (AMD) vs nVidia: We still spec nVidia because we don't have problems with its OpenGL-X driver under linux. Perhaps ATI has finally supplied one that works, but this hasn't been attempted in a couple years. ATI cards on the Mac work fine with freesurfer though. /// * /GPU: We no longer support [further] CUDA or GPU development because of lack of resources and difficulty, in preference to using OpenMP, which uses CPU cores. We will continue to support the existing GPU CUDA code that runs on recon-all with the -use-gpu switch. By support, keeping it running with each new nvidia cuda driver release as best as we can./ Is this still accurate? The Tech support at my university would order an AMD graphics card, since the issue with the drivers for Linux seems to be fixed. Does anyone has any current experiences with AMD vs. nVidia graphics cards? Thanks in advance and best wishes, Falko

3 2

Confusion about PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
by 周冬跃 23 Sep '21

23 Sep '21

External Email - Use Caution Dear FreeSurfer experts: I use the command recon-all qcache to get file sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file. And I am confused that the cortical thickness in this file is measured in common space after sub is aligned with the common coordinate system or just measured in subject space after changing the vertex location in subject space? In other words, when a sub is aligned to the common coordinate system,the folding patterns changed.But I am not sure if the value of cortical thickness measures has been changed during this process? Best wishes！

1 0

thesegment_T1.sh error
by Szulia Agata 23 Sep '21

23 Sep '21

External Email - Use Caution Hi, I’m trying to run thesegment_T1.sh command on centos 7 in docker (fs 7.2.0). I have matlab v2014b installed in fs there. The subjects were successfully put through recon-all on mac Big Sur (also fs 7.2.0 but matlab does not want to work with Big Sur). I don’t know what to do with the error I get with every recon-all’d subject: Smoothing mesh collection with kernel size 0.750000 ...Smoothing class: 0 /usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 797 Killed /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML bmat1 /usr/local/freesurfer/subjects 0.333333333333333333333333333333333333 /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr /usr/local/freesurfer/bin/' 0 Linux 3520b46e7a14 5.10.47-linuxkit #1 SMP Sat Jul 3 21:51:47 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Thu Sep 16 23:20:28 UTC 2021 For more details, see the log file /usr/local/freesurfer/subjects/bmat1/scripts/hippocampal-subfields-T1.log If any one of you has run into this kind of problem or know how to solve it, I’d be happy to hear your thoughts. Kind regards, Agata Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są poufne i podlegają ochronie prawnej. Jeśli nie jesteś jej prawidłowym adresatem, jakiekolwiek wykorzystanie w tym zapoznanie się z treścią przesłanych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne rozpowszechnienie, są ściśle zabronione. Jeśli otrzymał/a Pan/i niniejszy przekaz wskutek błędu, proszę o niezwłocznie powiadomienie nadawcy i usunięcie otrzymanych informacji. Kontakt: Uniwersytet Medyczny w Łodzi, 90–419 Łódź, Al. Kościuszki 4, Rektorat – Centrala, Tel. 42 272 59 66 umed.lodz.pl Confidentiality Notice - This e-mail is confidential, may be legally privileged. If you are not the intended recipient, you may not use, disclosure, distribute, copy, print or rely on this e-mail. If you received this e-mail in error, please notify the sender and delete the material from any computer.Contact:Medical University of Lodz, 90–419 Lodz, POLAND, 4 Kosciuszki Avenue, Rector’s Office, phone 0048 42 272 59 66 umed.lodz.pl

2 3

← Newer
1
2
3
4
5
6
7
8
...
11
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 September 2021