Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

mean cortical thickness not equal to averaged ROIs cortical thickness
by Nabin Koirala 30 Jun '16

30 Jun '16

Hi freesurfer team, I extracted the cortical thickness values using aparcstats2table command and I got the cortical thickness values for 34 regions and mean cortical thickness for each hemisphere. But when I averaged the cortical thickness from those 34 regions regions it was different than the mean cortical thickness obtained by aparcstats2table. I would expect it to be the same or very close but I checked it for more than 100 subjects and they are significantly different. Am I missing something silly here ? Thank you. Regards, Nabin

3 5

Get a given point's ROI
by Yuan Lin 29 Jun '16

29 Jun '16

Dear FreeSurfer experts, I am a beginner to learn to use FreeSurfer. Now I have a question to be solved. I have gotten the reconstruction results of a subject after using the command recon-all. How can I know a given point belongs to which region of interest? For example, how can I know whether a give point belongs to the superior frontal or inferior temporal? Which commands should I use? Thank you so much. Best, Lin

2 3

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arkadiy Maksimovskiy 29 Jun '16

29 Jun '16

Thank you for catching this. Really appreciate your help. - Arkadiiy

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28
by Arkadiy Maksimovskiy 29 Jun '16

29 Jun '16

Thank you!!

1 0

longitudinal tracula
by Harms, Michael 29 Jun '16

29 Jun '16

1 0

Announcement: fsurf, a command line tool for running freesurfer on the Open Science Grid
by Krieger, Donald N. 29 Jun '16

29 Jun '16

Dear FreeSurfer community, The Open Science Grid (http://www.opensciencegrid.org) is a federation of university and laboratory HPC facilities which share computing capacity to support science. We have developed a command line tool "fsurf" you can use from your laptop or desktop computer to submit scans for FreeSurfer processing on these clusters. In the initial release it is capable of executing "recon-all -all -i SubjectName.mgz" using FreeSurfer 5.3. No allocation is required. We only request that you cite the OSG in publications that benefit from its use. Instructions for getting started are found here: http://bit.ly/freesurferopensciencegrid. Please post questions and problems to OSG user support at user-support(a)opensciencegrid.org<mailto:user-support@opensciencegrid.org>. We hope you find it useful. Best regards, The OSG fsurf support team

1 0

No intensity command
by Sabrina Yu 29 Jun '16

29 Jun '16

Hello, I have a question about taking out the intensity normalization commands in recon-all. I want to eliminate all normalization steps so that the WM will not be set at an average of 110. Using the ReconAllDevTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable <https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable>), I took out all command flags related to intensity normalization. Are these commands correct? 1) I copied orig.mgz to generate nu.mgz, T1.mgz, norm.mgz. 2) recon-all -i <.nii file> -motioncor -talairach -skullstrip -s SUBJECT 3) recon-all -skullstrip -s SUBJECT 4) recon-all -gcareg -careg -calabel -maskbfs -segmentation -fill -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -s SUBJECT 5) recon-all -autorecon3 -s SUBJECT I hope that my question makes sense. Thank you in advance for your time. Sabrina

2 2

Re: [Freesurfer] Question about FreeSurfer
by Dorsa Haji Ghaffari 29 Jun '16

29 Jun '16

Hi, I am graduate student at the University of Michigan and I am performing research on deep brain stimulation. I want to warp an anatomical brain atlas to individual patient MRIs to get the patient specific brain models out of it. I chose FreeSurfer to do this and I have installed it on my computer. I realized that it takes 10-20 hrs to reconstruct the image. I wanted to ask if that is the time for one image? or the whole series of images? I also wanted to ask if there is a step by step tutorial on how to do this. Thank you > > Dorsa Ghaffari >

2 13

Motion values during structural run
by Rodriguez-Thompson, Anais 29 Jun '16

29 Jun '16

Hi Freesurfer Experts, Is there a way to calculate average displacement during a T1_MEMPRAGE scan (similar to using fmcpr.nii to calculate avg displacement during functional runs)? Thank you, Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

1 0

Tracula : ERROR: cannot unpack mosiacs without ASCII header
by Koubiyr, Ismail 29 Jun '16

29 Jun '16

Hi everyone, I’m reposting my problem if someone could help me I would really appreciate it. I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. P.S : DTIFIT works on FSL (FDT) but gives a poor quality in the reconstruction not as the one expected with Tracula. Thank you in advance for your help, Ismail

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