Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

recon-all error: cannot find or read /usr/local/freesurfer/dev//average/colortable_BA_thresh.txt
by Kelley, William 15 May '23

15 May '23

External Email - Use Caution Hello FreeSurfer Developers, Over the weekend I attempted to run a few mri images through recon-all on launchpad, but this morning I found the following error for each: ERROR: cannot find or read /usr/local/freesurfer/dev//average/colortable_BA_thresh.txt Here is the full recon-all command: recon-all -subjid $subject -all -brainstem-structures -no-isrunning I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this one? Also, I've attached one of the recon-all logs in case it's of any use. 1. FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20230515-068e824 2. Platform: CentOS 7 3. uname -a: Linux demeter.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4. recon-all.log: see attached

1 0

Reconstruction output differences with freesurfer 7.3.2 and 7.2.0
by Md Mahfuzur Rahman 15 May '23

15 May '23

External Email - Use Caution Dear Developers, I am trying to run 'recon-all' and then do some QC on the output. With 7.3.2 for skull stripping, I can fairly fix the brain mask with adjusting thresholds. But after fixing it, when I ran "recon-all -autorecon2 -autorecon3 -subjid <subject name>", the surface didn't change noticeably. However, I obtained noticeable changes with version 7.2.0. I am attaching a screenshot to make it understandable. Should there be output differences between 7.2.0 and 7.3.2? I was wondering if anyone has comments about which version one should rely on. Any help will be highly appreciated. Thank you. Regards, --- Mahfuz Md Mahfuzur Rahman, Ph.D. Postdoctoral Research Associate (AC) Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University Email: mahfuz.gsu(a)gmail.com, mrahman21(a)gsu.edu

1 0

Issue with running recon-all
by hmarzban＠student.ubc.ca 15 May '23

15 May '23

External Email - Use Caution Dear developers, I am writing to report an issue I encountered while running recon-all on some subjects. Specifically, I received an error message stating "error: freadFloat: fread failed" for several of the subjects. Starting surface-based mapping Reading source registration /arc/project/3T/fsaverage/surf/lh.sphere.reg error: freadFloat: fread failed error: freadFloat: fread failed ... I am wondering if any of you have experienced this issue before, and if so, I would greatly appreciate any recommendations on how to proceed with resolving it. Thank you for your help. Hengameh

2 1

Individualized subcortex atals generation with freesurfer derivatives
by bong516612 15 May '23

15 May '23

2 1

EasyReg Troubleshoot - Killed
by Nadia Kane 12 May '23

12 May '23

External Email - Use Caution Hi, I'm working on applying deep learning in image registration for a master's project. The overarching goal was to use real tissue clearing lightsheet data to perform the image registration, but first created some synthetically deformed brains based on the Allen Brain Atlas and Lab2im algorithm <https://secure-web.cisco.com/15MqNxXe5KXHPIE2voNOwPZsAQlEcjvJ2VaFxWcPmWFuUF…>. However, I'm having some issues implementing the command in an Centos Linux 7 (Core) HPC environment. The command gets Killed, I'm wondering if you could provide some more insight? Thank you! I've set up my environment as follows: module load mamba mamba create -n freesurf # I named the environment freesurf conda activate freesurf mamba install tensorflow-gpu cuda-version=11.8 I've attached the easyreg.sh shell script that I run. Here's the output: (freesurfer) kanex161@agc02 [~/Documents/Thesis/code] % bash easyreg.sh 2023-05-09 11:19:32.374206: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-09 11:19:32.405672: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-09 11:19:32.405981: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-05-09 11:19:33.258226: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT [W interface.cpp:47] Warning: Loading nvfuser library failed with: Error in dlopen: libnvfuser_codegen.so: cannot open shared object file: No such file or directory (function LoadingNvfuserLibrary) using 1 thread Segmenting reference image Reading reference image Setting up segmentation net 2023-05-09 11:19:38.489093: E tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:266] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected 2023-05-09 11:19:38.489166: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] retrieving CUDA diagnostic information for host: agc02 2023-05-09 11:19:38.489202: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname: agc02 2023-05-09 11:19:38.489460: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda reported version is: 470.103.1 2023-05-09 11:19:38.489502: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel reported version is: 470.103.1 2023-05-09 11:19:38.489530: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel version seems to match DSO: 470.103.1 Inference / segmentation easyreg.sh: line 8: 1108392 Killed ./mri_easyreg --ref /home/umii/kanex161/Documents/Thesis/data/outputs/atlas/atlas.nii.gz --flo /home/umii/kanex161/Documents/Thesis/data/outputs/lab2im/brains/brain_00.nii.gz --ref_seg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/ref_seg.nii.gz --flo_seg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_seg.nii.gz --flo_reg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_reg.nii.gz --fwd_field /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/fwd_field.nii.gz

2 2

password
by m.77 ms77 12 May '23

12 May '23

External Email - Use Caution Sorry, I have a problem. I am using FS_7_2_0_ubuntu_18_04_06.ova.7z on my virtual machine system but it wants a password to open it. What's the password of this file? Thank's

1 0

recon-all for GM quantification
by Nikolaidou, Sofia 12 May '23

12 May '23

External Email - Use Caution Good afternoon, My name is Sofia and I work with Drs. Eva Ratai and Lilly Mujica-Parodi on the DCC project. I am reaching out to ask for your advice on a FreeSurfer question. I am using recon-all to try to quantify and compare GM volume and mean thickness among our subjects. In essence, I think I have all the necessary measurements in the outcome files titled aseg.stats and ?h.aparc.stats. Would you happen to know how I can customize the stream and reduce the processing time by taking out steps from the -all process? In other words, what would be the minimal set of steps that I have to run in order to acquire the above output files? Thank you in advance! Kindly, Sofia Sofia Nikolaidou | Clinical Research Coordinator MGH/HST Martinos Center for Biomedical Imaging 149 13th St, Charlestown, MA 02129 Phone: 617-417-4463 snikolaidou(a)mgh.harvard.edu

2 1

Password
by m.77 ms77 12 May '23

12 May '23

External Email - Use Caution I am attempting to use FreeSurfer on Windows via VirtualBox following this tutorial: https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWA… < https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWA… >Can I ask for the password that is required to log in Ubuntu when using the FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1lKTuilXtq3B8-EfyzhLjRyYTSJz3W6yULKYFbuWJuM2T8…> provided in the tutorial? Thank you very much

1 0

Cannot find subject for recon-all
by Pedro henrique barradas 12 May '23

12 May '23

External Email - Use Caution Hello! I have recently installed freesurfer and was attempting to reconstruc some exams but I keep getting this error message Pedros-Air:subjects pedrobarradas$ recon-all -i 01.nii. -s test1 -all ERROR: cannot find 01.nii. recon-all -s exited with ERRORS at Mon May 1 16:51:37 WEST 2023 For more details, see the log file To report a problem, see http://secure-web.cisco.com/19U7LOcdijBY9U_PmLfURFHEhzJ_eruNexkDUwOwlgl3hTF… I'm not sure what I am doing wrong. Any help would be tremendousy appreciated. Best Wishes Pedro Barradas

2 3

Freesurfer 7.4.0 (May 2023) distribution now available
by fsbuild 11 May '23

11 May '23

External Email - Use Caution The 7.4.0 (May 2023) Freeusrfer distribution is now available online. See the release notes for new features and fixes,https://secure-web.cisco.com/17pXU7bQr7zSbi9r9UmzQuVuj4ve9RgXhkd4VScO… See the download page for the links to available packages,https://secure-web.cisco.com/10-c3tNib37MYk25YtbeshZSn0IrQt-b8Pwzo… - R.

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer