Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Labels to annotation
by Karen Marie Sandø Ambrosen 23 Jun '14

23 Jun '14

Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: "WARNING: vertex 6021 maps to multiple labels! (overwriting)", and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings? I do the operations (volume labels-->surface labels-->annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations? Best, Karen

4 4

Project probabilistic connectivity maps to pial and calculate mass center
by gong jinnan 23 Jun '14

23 Jun '14

Dear all, I have used probabilistic tractography methods by FSL-FDT to get probabilistic connectivity between grey-white matter interface of precentral and basal ganglia in subjects’ space. The latter one was used as classification mask. And then all of tractography maps were registered to MNI space. Now I want to project tractography results like seed_to_BG.nii.gz to pial in Freesurfer and calculate mass center of those maps. But unfortunately I am not clear how to do that. So there is my question: 1.It is not difficult to project seed_to_BG.nii.gz to .../mri/orig.mgz. But how to project to pial after that? 2.How can I get mass center like pictures in attachment. I tried calculated mass center of seed_to_BG.nii.gz in MNI space, but the mass center point does not fall in precentral. So I want to do that in pial. 3.How to transform subjects’ pial to talairach pial? I searched method to do that for a long time, but have no idea yet. So I hope I can get valuable suggestions here. I will be grateful if you can help me! Sincerely， Jinnan Gong Best wishes for you! Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China

2 1

Group analysis over different studies?
by Terri Scott 23 Jun '14

23 Jun '14

Hi all, I want to do a group analysis using subjects that were run in different studies but who have (some of) the same relevant functional contrasts. Is there a way to run something like isxconcat-sess on data from different analysis streams? Or if not, which files do I need to collect and align from each subject in order to run mri_glmfit? What would be the best way to handle this analysis? Thanks, Terri

3 3

Using QDEC for 3 groups x 2 time-points
by Tudor Popescu 23 Jun '14

23 Jun '14

Dear FS list, I have a data set with 3 groups (2 treatments, 1 control), each with equally-spaced time-points (pre and post structural scan). I've done the 3 longitudinal pre-processing steps, and stage#1 of the two-stage model, and I would prefer to run stage#2 (cross-sectional analysis of the difference) with QDEC as opposed to with mri_glmfit. I know that QDEC is meant for 2 groups, but I see that designs with 4 or 6 groups can be analysed with QDEC (as per this <https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples> FSGD examples page) whereas designs with 3 groups cannot be. It seems to me that an even number of groups is QDEC-able while an odd number isn't, but is there any workaround so that I can still use QDEC? Perhaps if I only do pairwise comparisons one at a time, i.e. treatment1 vs control and treatment2 vs control? Many thanks! Tudor

3 5

low polygon count like fsaverage3
by Kai Schlamp 23 Jun '14

23 Jun '14

Hello again, I am still looking for a way to create a low polygon surface during recon-all (where labels still fit). Is there any (expert) option where I can specify the number of vertices or distance between vertices? How was fsaverage3 (very low polygon count) was created? Best regards, Kai

2 1

Alzheimer's Disease Sage/DREAM Challenge
by Arno Klein 22 Jun '14

22 Jun '14

The Alzheimer's Disease Sage/DREAM Challenge #1 (AD#1) launched earlier this month! The goal of the AD#1 is to apply an open science approach to rapidly identify accurate predictive AD biomarkers that can be used by the scientific, industrial and regulatory communities to improve AD diagnosis and treatment. AD#1 will be the first in a series of AD Data Challenges to leverage genetics and brain imaging in combination with cognitive assessments, biomarkers and demographic information from cohorts ranging from cognitively normal to mild cognitively impaired to individuals with AD. FreeSurfer was instrumental in the processing of the image data. For challenge details, please see: https://www.synapse.org/#!Synapse:syn2290704 Cheers, @rno

2 1

Postdoc opening in multimodal human brain mapping/modulation & epilepsy
by David Groppe 22 Jun '14

22 Jun '14

Post doctoral position available for research using a multimodal approach to investigate brain organization and function at the Hofstra University-North Shore LIJ School of Medicine in partnership with the Feinstein Institute for Medical Research. Studies involve surgical epilepsy patients undergoing intracranial electrophysiological monitoring for seizure detection and functional electrical stimulation mapping. Ongoing research projects include: 1) Validation of task-based and resting state fMRI and DTI using electrical stimulation mapping, electrocorticography and corticocortical evoked potentials; 2) Investigation of the neuronal dynamics underlying selective attention and active sensing, language, object identification and auditory stream analysis; 3) Modulation of neuronal function by direct cortical stimulation and investigation of the mechanisms of TMS, tDCS and tACS; 4) Prediction of seizure spread using electrophysiological and MRI markers. Responsibilities will include designing fMRI, ECoG and neurostimulation experiments and data analysis and the coordination of access to patients for research studies. Located in Long Island, 10 miles from Manhattan, there is tremendous opportunity for involvement with collaborative effort with multiple research groups the area with similar interests. Candidates should have M.D. and/or Ph.D. degrees and have some background in fMRI, electrophysiology, and/or data analysis (Matlab). Ideal start date would be between 9/2014-1/2015. For more information about the lab see: http://www.feinsteininstitute.org/faculty/ashesh-mehta-md-phd/ If interested, please submit CV and short statement of interest to Dr. Ashesh Mehta at amehta(a)nshs.edu for more information. -- David Groppe, Ph.D. Institute Scientist Laboratory for Multimodal Human Brain Mapping Feinstein Institute for Medical Research Manhasset, New York http://www.cogsci.ucsd.edu/~dgroppe/

1 0

Why the result was not same for the same subject
by wangkangcheng_gmail 21 Jun '14

21 Jun '14

Dear experts I used freesurfer (Version 5.3) to calculate one subject for ten times and extract the number of each index. However, I found that the number was different each time. Is this normal? Why the result was not same for the same subject? Thank you Wang Kangcheng

2 1

MatLab Version and Hardware and Freesurfer Statistics
by Pedro Rosa 20 Jun '14

20 Jun '14

Dear list, Does the OS version, hardware or MatLab version (i.e., 2013a vs. 2014a) impacts in the results from the LME processing (Bernal-Rusiel et al.), employed after the Freesurfer 5.1/5.3 longitudinal pipeline? Regards, Pedro Rosa.

1 0

FreeSurfer Question
by Shazia Dharssi 20 Jun '14

20 Jun '14

Hi, I was wondering if you happened to know why the origin of the rawavg.mgz image is slightly different than the origin of my original structural image that I "recon"ed to obtain processed FreeSurfer data. Am I doing something wrong or is this expected? Is there an image that FreeSurfer creates that is has the exact dimensions and origin as my original data? Thank you in advance for all of your time and help! Best, Shazia -- *Shazia Dharssi* Columbia University Medical Center Department of Neurology Taub Institute P: (212) 305-8921 C: (319) 431-5060

2 1

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