Freesurfer January 2023

freesurfer@nmr.mgh.harvard.edu

87 participants
111 discussions

Re: [Freesurfer] dicom reading errors
by fsbuild 18 Jan '23

18 Jan '23

External Email - Use Caution The output shows the command running on Ubuntu 18 linux and getting an error from the shell for a bad file descriptor (fd),Linux holowach 5.3.0-53-generic #47~18.04.1-ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x85_64 x86_64 GNU/Linuxsh: 1: Syntax error: Bad fd numberThat could be an issue with the shell on Ubuntu.   On Ubuntu the default “sh” in PATH, $ which sh/bin/sh - is usually a soft link to the minimal “dash” shell and not a more complete shell like the “bash” shell. $ ls -l /bin/shlrwxrwxrwx 1 root root 4 Jan 3  2020 /bin/sh -> dash* I would try using the bash shell, e.g., type “bash” in your terminal window and then run the command that produced the error, $ bashyourhostname[0]:~$… run your command ... If that fixes the issue, you might consider changing the /bin/sh link to point to bash instead of dash.  But you will need sudo/root privileges to do that, e.g., $ cd /bin$ sudo rm sh$ sudo ln -s bash sh - R. On Jan 18, 2023, at 14:36, Alexopoulos, Dimitrios <dimitriosalexopoulos(a)wustl.edu> wrote:

1 0

dicom reading errors
by Alexopoulos, Dimitrios 18 Jan '23

18 Jan '23

External Email - Use Caution Trying to run FS7.2. on a dataset and am getting dicom errors as shown below. Looks like some issues related to dicom compression and bad fd number. Any suggestions from the FS experts please? Jim [cid:image001.jpg@01D92B41.E39EE410] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

TRACULA trac-all error
by Nita Akoh 18 Jan '23

18 Jan '23

External Email - Use Caution Hey, I'm trying to run "trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial" but keep getting this error : /shared/centos7/freesurfer/7.3.2/bin/free/sources.csh: No such file or directory. My colleague ran this step on the same data and it worked for her but not for me. We load the same freesurfer version and use the exact same commands. Thanks, Nita Akoh Candidate for B.S in Behavioral Neuroscience & International Affairs College of Science Northeastern University +17165011641| Akoh.n(a)northeastern.edu

2 1

Two basic questions: brainmask file versions and qcache
by Harriott, Emily M 18 Jan '23

18 Jan '23

External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all well. I have two relatively basic questions that I am hoping to get some help with. My basic planned processing pipeline is: Run initial recon-all with gcut and ws flags Edit white matter/pial voxels and add control points (as needed) Run second recon-all with autorecon2 and autorecon3 flags Run LGI I have two questions about this: When I run the initial recon-all, I end up with three versions of the brainmask within the /mri/ folder: brainmask.auto.mgz, brainmask.gcuts.mgz, brainmask.mgz. Which brainmask version do I edit, so that my edits are incorporated into the second recon-all run and thus the second attempt at wm/gm segmentation is better? When and with what command(s) do I use the qcache flag? I apologize that these are quite basic, but sincerely appreciate any input anyone might be able to provide. Thank you so very much in advance! All the best, Emily Harriott Doctoral student at Vanderbilt University

1 0

Re: [Freesurfer] PetSurfer - MG coregister
by Marina Fernández 18 Jan '23

18 Jan '23

External Email - Use Caution Dear Rahul, I just used the wiki of the Freesurfer functions, the information is very complete. If you want to use Freesurfer, you can start by doing the cortical reconstruction process for each subject ( https://secure-web.cisco.com/1Lj_XzmtE_iAYreTtmjwq2Q0VTCaZWdcX4QFapQPQO_Y7j…) and then prepare the maps to do the analysis that interests you. In the case of PET analysis, you can follow the steps explained on the PetSurfer wiki ( https://secure-web.cisco.com/1SUsUq0XwDtpjwx2dSpE1KOdwDPRl2MG5fyhegdBeDHaK3…) If you have any particular questions about feature options, you can search this list if other users have asked before. In case the question is not resolved, you can ask it here so that the experts can answer you. I hope it helps. Cheers, Marina.

2 1

New Postdoc Position on Brain Connectivity at Karolinska Institute - Deadline 22/01/2023
by Joana Braga Pereira 17 Jan '23

17 Jan '23

External Email - Use Caution Dear all, We are looking for another new Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms and biofluid assays to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Associate Professor Joana B. Pereira and Assistant Professor/Neurologist Sara Garcia-Ptacek and it will involve analyzing the effects of different types of medication on brain connectivity in patients at different stages of Alzheimer's disease. The Postdoctoral fellow will work in the center of Stockholm together with 3 PhD students, 2 Postdocs and 4 affiliated members of Dr. Pereira's group. He/she will help collect data from patients at the local memory clinic using well-established and new imaging sequences as well as perform analyses using already acquired cross-sectional and longitudinal data. We work in a friendly and inclusive environment, where the future fellow will be involved in many projects, collaborate with group members on different studies, learn new skills, attend conferences, apply for grants and develop a wide network of international collaborations. The ideal candidate should have the following qualities: - A PhD in medicine, neuroimaging, computational science, physics, neuropsychology, statistics or a related field. - Experience in statistical techniques, programming, and scripting in MATLAB, STATA, Python, R or other softwares. - Experience with structural MRI, DTI, fMRI and/or EEG/MEG imaging analyses. - Experience with different softwares such as SPM, FSL, FreeSurfer, AFNI, etc. - Experience or interest in working with aging and/or neurodegenerative disorders, particularly Alzheimer’s and Parkinson’s diseases. - Good academic record with scientific publications in world-class journals. - Be independent and willing to supervise students. The Postdoctoral studies will be performed for 2 years, with possible extension for an additional year. To apply please go to: https://secure-web.cisco.com/1ck5sqkXIvnbFkdYGa5YGhpitAhn4cXIxrXSU25TPI75Bo… (Deadline: 22.Jan.2023) For further information or general inquiries, please contact Joana B. Pereira at joana.pereira(a)ki.se. Best wishes, Joana

1 0

use specific tools from dev-version on cluster
by AmirHussein Abdolalizadeh 17 Jan '23

17 Jan '23

External Email - Use Caution Hi all, I am willing to use mri_synthseg and mri_easyreg which are available in the 7-dev version on a high-performance cluster. Is there a way to do it without installing the 7-dev version on it? I didn't have enough RAM space to do them on my local machine. Best, Amir

1 0

VM file password
by Kern, Simon 17 Jan '23

17 Jan '23

External Email - Use Caution Dear Mailinglist, I would like to request the password for the vmware gz file. I was referred to this mailing list. Could you send me the password? I already have a license file. Best regards, Simon Kern -- [1570451663583] Simon Kern MSc Artificial Intelligence / BSc Cognitive Science PhD candidate Department of Clinical Psychology RG Psychology and Neurobiology of Sleep and Memory Central Institute of Mental Health J 5 · 68159 Mannheim, Germany Phone: + 49 17656774775 simon.kern(a)zi-mannheim.de<mailto:simon.kern@zi-mannheim.de> http://secure-web.cisco.com/1w78yI8LpZREd0df3OuMf1_mRT77p5wfwcmi6hOKVS__QLZ… <http://secure-web.cisco.com/1pn2Tt_MljUeP7ZoJC_PS4GMa9ssBkRA_00FpXOquRAeFk1…>Executive Board: Prof. Dr. Andreas Meyer-Lindenberg, Dr. Matthias Janta President of the Supervisory Board: Dr. Carsten Dose

1 0

trac-all -prep early stage errors
by Simonas Jesmanas 14 Jan '23

14 Jan '23

External Email - Use Caution Hello everyone, I am having trouble getting past the very first stages of trac-all -prep. I am using FreeSurfer 7.3.2. I tried several workarounds based on previous answers to similar problems in this mailing list, but I am unsuccessful each time. First, when I try to run trac-all -prep without any configuration file, using only the defaults, it prints out an error: trac-all -prep -s sub-01 -i $SUBJECTS_DIR/raw/sub-01/dwi/1_0000.dcm ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction As I understand it, the default version of trac-all should assume default deb0=0, and not look for reverse-polarity images to do distortion correction for TOPUP. Then, I tried to perform the analysis using the configuration file and specify that I do not want to perform correction based on reverse-polarity images or phase maps (my data don't have these), by explicitly entering "set dob0 = 0". The problem persisted. I did what a previous user was told to do - set "pedir" and "epifactor" and "echospacing" manually. Then, I ran into the final error which I cannot overcome. No matter what I do, it ends in an error: mv: cannot stat '/home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz': No such file or directory It seems it cannot create this file. Earlier in the log there is also a previously mentioned error: INFO: input image orientation is LPS INFO: input image determinant is 6.49902 mri_convert -oni 128 -onj 128 -onk 60 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc 0 -21 7 -rt nearest /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig.1.nii.gz /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 128 -onj 128 -onk 60 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc 0 -21 7 -rt nearest /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig.1.nii.gz /home/sj/freesurfer/DEPRINFL_subjects_outputs/sub-01/dmri/dwi_orig_las.1.nii.gz mri_convert: directions must have non-zero magnitude; out_i_direction = (0, 0, 0) It appears to be a problem with converting into LAS. (Previously there was mention of there being a wrong "trac-preproc" file for runs with only 1 subject, but my problem remains when trying to run single and multiple subjects. I also tried to change my trac-preproc file to the versions from previous answers, with no luck). When I check the dmri folder the dwi_orig.1.bvals and dwi_orig.1.bvecs, and dwi_orig_las.1.bvals files contain correct values, but dwi_orig_las.1.bvecs contains only zeros. When I run mri_info on dwi_orig.1.nii.gz I get this: Volume information for sub-01/dmri/dwi_orig.1.nii.gz type: nii dimensions: 128 x 128 x 60 x 76 voxel sizes: 1.718750, 1.718750, 2.200000 type: SHORT (4) fov: 220.000 dof: 1 xstart: -110.0, xend: 110.0 ystart: -110.0, yend: 110.0 zstart: -66.0, zend: 66.0 TR: 7100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 76 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9959, y_r = -0.0243, z_r = -0.0868, c_r = -0.4050 : x_a = 0.0326, y_a = -0.9949, z_a = -0.0955, c_a = -21.6846 : x_s = -0.0841, y_s = -0.0979, z_s = 0.9916, c_s = 7.5075 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.7117 -0.0418 -0.1910 117.5550 0.0561 -1.7100 -0.2100 90.4641 -0.1445 -0.1683 2.1816 -37.9249 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 6.49902 ras to voxel transform: -0.5794 0.0190 -0.0489 64.5443 -0.0142 -0.5789 -0.0570 51.8698 -0.0395 -0.0434 0.4507 25.6592 0.0000 0.0000 0.0000 1.0000 "PhEncDir" shows UNKNOWN, but as I said, my config file contains "set pedir = (AP)". I also tried to do the analysis on FreeSurfer 7.2 and the develeopment version, but no luck. I would appreciate any input into how to solve this problem. Regards, SJ.

1 0

Password for Virtual Box Installation
by Nathanial Osterhout 14 Jan '23

14 Jan '23

External Email - Use Caution Hello, I'm trying to install the Ubuntu image with Freesurfer preinstalled and it is asking for a password that I do not have. If I could get that passcode it would be greatly appreciated. Thanks

1 0

← Newer
1
...
4
5
6
7
8
9
10
11
12
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 January 2023