Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

Cortical thickness of elephant brain
by Malav Shah 09 Jun '23

09 Jun '23

External Email - Use Caution Dear freeSurfer team, I am trying to extract cortical thickness in a postmortem elephant (structural) MRI scan. I initiated the process with the segmentation of white (wm) and pial matter, using MATLAB image processing tools. Having satisfied white and pial matter labels, I "tesselated" these volumes to generate pial and wm surfaces. Then, with 'mris_smooth' command, I smoothed these surfaces. When attempted to estimate cortical thickness between these surfaces (lh.pial.smth5 and lh.wm.smth5), I get the following error. command: mris_place_surface --thickness lh.pial.smth5 lh.wm.smth5 20 5 lh.thickness error: No such file or directory error: ERROR: MRISreadVertexPositions(/Volumes/experiment/share/Malav/Ele_ana_cortexMRI/pipelines/dumba_piece/lh.wm.smth5): surfaces differ. Main: 177753 verts 365096 faces, lh.wm.smth5: 145095 verts 298436 faces Surfaces may be out-of-date I understand there is a mismatch in the number of nodes of these surfaces. How can I rectify this issue to get to the thickness? Thanks and regards, malav Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

2 6

different results for gtmpvc with different tracers
by Federica Di Antonio 09 Jun '23

09 Jun '23

External Email - Use Caution Dear experts, I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer. Do you think this error can result from previous errors in the analysis? Or is it in some way plausible? Thank you for your patience, Federica

2 4

trac-all error aparc+aseg_mask.bbr not found
by Stylianos Charalampous 07 Jun '23

07 Jun '23

External Email - Use Caution Hello, I am attempting to run white matter tractography using TRACULA, as described in the tutorial, however, using my own data and brain parcellation acquired using external algorithm. I have put the aparc+aseg.mgz file in the subject directory in folder mri but I am getting the following error: Error : No image files match: /diffusion/root/subject/visit/dlabel/diff/aparc+aseg_mask.bbr The error occurs when running the tensor fit step using the prep command: trac-all -c config_file -prep As described in the trac-all documentation (https://secure-web.cisco.com/1OCcv-f3jRdcpwsIbW4XJ0lMpQY1t0rNu6Ec3x47wJ56GO…) the file aparc+aseg_mask.bbr was supposed to be created by the intra step which comes before tensor-fit but upon checking nothing is created. I have also tried running only that specific step using trac-all -intra but nothing is created either. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this one? 1) FreeSurfer version: freesurfer-7.3.2 2) Platform: ubuntu-22.04.02

1 0

Calculate cortical thickness of a volumetric ROI
by Carlos Alcocer 07 Jun '23

07 Jun '23

External Email - Use Caution Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using https://secure-web.cisco.com/1SRB1kl1prYOxcV3133JRM9O5Bj21w9M9aZYfcod7MM5GH… as a guide. Since, I already have the volumes in subject space. I did a modified pipeline and only did the following for each subject: 1. mri_vol2surf --mov /path/to/ROI5.nii --regheader --projfrac-max 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh 2. mri_segstats --seg $SUBJECTS_DIR/subjid/surf/lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt Does this make sense? Also, separately, is the volume that is also computed in this method accurate? I noticed that the volume is always equal to the number of voxels, which I assume a voxel is equal to 1mm^3? However, when looking at aseg.stats these volumes have different values from their number of voxels. Thank you, Carlos

1 0

Volume files for clinical pipeline
by KennethSPrice 06 Jun '23

06 Jun '23

External Email - Use Caution Hello Freesurfers! I'd like to compare volumetric changes in two groups and visualize the difference on an overlay of fsaverage. But there are no volume files to concatenate and compare. How do I run a volumetric analysis using FSGD or QDEC without the volume files from recon-all_clinical? Thanks, Ken

1 0

Password Freesurfer VirtualBox Image
by Michael 06 Jun '23

06 Jun '23

External Email - Use Caution Hello! I kindly ask for the VM_67 VirtualBox Image password. Thank you so much! Best, Michael

1 0

Request for Password to unzip FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Kazuki Sakakura 05 Jun '23

05 Jun '23

External Email - Use Caution Dear developers, I kindly request a passcode to unzip FS_7_2_0_Ubuntu_18_04_06.ova.7z. Sincerely, Kazuki Sakakura, MD, PhD Research Scholar, Wayne State University Address: 3901 Beaubien Street, Detroit, Michigan, 48201, USA.

1 0

Re: [Freesurfer] cannot find freesurfer folder
by fsbuild 04 Jun '23

04 Jun '23

External Email - Use Caution Please check your email/spam filters as you were sent the info for the VM earlier today. The freesurfer_7.2.0_amd64.deb file will install 7.2.0 as /usr/local/freesurfer/7.2.0, but there is no need to that in the VM because it should already be installed there. - R. On Jun 4, 2023, at 11:31, Pedro henrique barradas <phbarradas(a)hotmail.com> wrote:        External Email - Use Caution        HelloI tried installing freesurfer through ubuntu but I can not understand where it has been instaled nor  can I find the source file. can anyone help please?

1 0

cannot find freesurfer folder
by Pedro henrique barradas 04 Jun '23

04 Jun '23

External Email - Use Caution Hello I tried installing freesurfer through ubuntu but I can not understand where it has been instaled nor can I find the source file. can anyone help please? I am trying to install with a virtualbox but I need a passcode to unzip the file pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'freesurfer' instead of './freesurfer_7.2.0_amd64.deb' freesurfer is already the newest version (7.2.0). The following packages were automatically installed and are no longer required: efibootmgr libefiboot1 libefivar1 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ cd freesurfer -bash: cd: freesurfer: No such file or directory pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ pwd $FREESURFER_HOME /mnt/c/Users/phbar/Desktop pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ echo $FREESURFER_HOME pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb [sudo] password for pedro: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'freesurfer' instead of './freesurfer_7.2.0_amd64.deb' freesurfer is already the newest version (7.2.0). The following packages were automatically installed and are no longer required: efibootmgr libefiboot1 libefivar1 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. pedro@DESKTOP-0IOF7IK:/mnt/c/Users/phbar/Desktop$ [https://secure-web.cisco.com/1b-Yh_XBB5RIegXXHi7o45IHWi1ofOMHmN79tn6_xj3GCj…]<http://secure-web.cisco.com/19tyssBrpamrK0eOnbMfTrJ66_s4XP0-581Fw-9rA_kIhY9…> Sem vírus.http://secure-web.cisco.com/15e5A5-l5iw1W96sl0rIE2bIKpt8EjCXtYl0e3OPo…<http://secure-web.cisco.com/19tyssBrpamrK0eOnbMfTrJ66_s4XP0-581Fw-9rA_kIhY9…>

1 0

Pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Pedro henrique barradas 04 Jun '23

04 Jun '23

External Email - Use Caution Hi I would like to request a passcode to unzip FS_7_2_0_ubuntu_18_04_06.ova.7z Thank you Pedro Barradas

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer June 2023