Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

How to make grey matter edits
by Rosalia Dacosta Aguayo 11 Jan '19

11 Jan '19

External Email - Use Caution Dear FreeSufer team, I have been working with MS patients using T1 lesion filled images. I corrected pial surface and I did control points for white matter. However, I have not found how to edit gray matter segmentation. I would much appreciate if you tell me where I could find a TUTORIAL fir this issue. Best regards, Rosalia

2 3

Questions About Effect Sizes in Vertexwise GLM Anlaysis
by Max Owens 11 Jan '19

11 Jan '19

External Email - Use Caution Hi Freesurfer Experts, I have two related questions about the measures of effect size that can be derived from a vertexwise GLM analyses conducted in Freesurfer: 1. What is the unit of effect size for the gamma.mgh file created by vertexwise GLM Analysis using mri_glmfit? 2. Based on two previous posts ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52144.html and https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57316.html) I tried to calculate Cohen’s d in all significant clusters resulting from clusterwise multiple comparison correction of a vertexwise GLM using mri_glmfit. I did this by dividing the gamma.mgh file by rstd.mgh to create a cohensd.mgh file (fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh). Then from the output of that operation I extracted the mean value in each significant cluster from my vertexwise analysis using mri_segstats (mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --o sum.dat). My understanding was that this would yield the average Cohen’s d of each cluster. However, if it is indeed Cohen’s d the effect sizes yielded (between .01 and .02) are so small that they should be undetectable given my sample size (N=1104). This leads me to believe that the outputs are not in fact the average Cohen’s d of the cluster. Can anyone provide any clarification of what the output file of this process means? Specifically, what is the unit of effect size? Thanks in advance for your help! Max

2 3

Re: [Freesurfer] Running TRACULA
by Yendiki, Anastasia 11 Jan '19

11 Jan '19

Hi Ainara - What do you mean by default freesurfer files? Can you describe how you created each subject's recon-all style directory under SUBJECTS_DIR? TRACULA looks for $SUBJECTS_DIR/$subjectid/mri/aparc+aseg.mgz for each subject ID. a.y On Jan 11, 2019 8:30 AM, Ainara Gomez <ainara.ggastiasoro(a)deusto.es> wrote: External Email - Use Caution Dear Freesurfer experts, I am trying to run TRACULA as a complementary analysis on a patients and healthy controls sample. I have read in the tutorial that it is assumed that FreeSurfer has already been run on all the subjects' T1-weighted data because TRACULA will use the aparc+aseg.mgz from each subject's FreeSurfer reconstruction. However, T1s of my subjects are not available for this study and I only have the diffusion images. I have run the three steps of the trac-all separately (using the default freesurfer files: aseg+aparc.mgz...) and all the processes have ended without errors. Is this correct? Is it possible to use the default freesurfer files instead of each subject's recon-all files in order to run trac-all? Thank you very much in advance, Ainara -- Ainara Gómez Gastiasoro Dpt of Methods and Experimental Psychology Neuropsychology of Severe Medical Conditions research team Faculty of Psychology and Education University of Deusto neurolab.deusto.es<http://neurolab.deusto.es/> https://twitter.com/deustoneurolab Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) <tel:%2B34%20944139000>

2 1

Running TRACULA
by Ainara Gomez 11 Jan '19

11 Jan '19

External Email - Use Caution Dear Freesurfer experts, I am trying to run TRACULA as a complementary analysis on a patients and healthy controls sample. I have read in the tutorial that it is assumed that FreeSurfer has already been run on all the subjects' T1-weighted data because TRACULA will use the aparc+aseg.mgz from each subject's FreeSurfer reconstruction. However, T1s of my subjects are not available for this study and I only have the diffusion images. I have run the three steps of the trac-all separately (using the default freesurfer files: aseg+aparc.mgz...) and all the processes have ended without errors. Is this correct? Is it possible to use the default freesurfer files instead of each subject's recon-all files in order to run trac-all? Thank you very much in advance, Ainara -- Ainara Gómez Gastiasoro Dpt of Methods and Experimental Psychology Neuropsychology of Severe Medical Conditions research team Faculty of Psychology and Education University of Deusto neurolab.deusto.es https://twitter.com/deustoneurolab Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3268) <%2B34%20944139000>

1 0

NeuroHackademy 2019
by Ariel Rokem 10 Jan '19

10 Jan '19

External Email - Use Caution We are happy to announce a call for applications to participate in Neurohackademy 2019! This two-week hands-on workshop held at the University of Washington eScience Institute in Seattle, July 29th - August 9th, 2019, focuses on tools and techniques used to analyze human neuroscience data, on methods used to extract information from large datasets of publicly available data (such as the Human Connectome Project, OpenfMRI, etc.), and on tools for making human neuroscience research open and reproducible. Neurohackademy sessions in the first week will include lectures and tutorials on data science, machine learning, data visualization, and data resources. The second week will be devoted to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. *For more details and a preliminary list of instructors, see: **https://neurohackademy.org/ <https://neurohackademy.org/>* We are now accepting applications to participate at https://neurohackademy.org/apply/ Ideally, applicants should have some prior experience with programming and with neuroscience data analysis, but we welcome applications from participants with a variety of relevant backgrounds. Accepted applicants will be asked to pay a fee of $200 upon final registration. This fee will include participation in the course, accommodation in the UW dorms, and two meals a day (breakfast and lunch), for the duration of the course. A limited number of fee waivers and travel grants will be available. We encourage students with financial need and students from groups that are underrepresented in neuroimaging and data science to apply for these grants (see application form for details). *Important dates:* *February 18th: Application deadline* *March 15th: Notification of acceptance* *April 1st: Final registration deadline*

1 0

LME MATLAB Tools
by Tefera, Getaneh B 10 Jan '19

10 Jan '19

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ .... To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)]; Based on the tutorial I run the following functions. rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig'); nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end; rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh'); [detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0); fs_write_Y(sided_pval,rhmri1,'spval.mgh'); When I view sig.mgh using tksurfer I see regions with red and blue color. 1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is larger than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file? With regards Getaneh

1 0

MRI sequence parameter difference and effect on cortical thickness values
by Arsenije Subotic 10 Jan '19

10 Jan '19

External Email - Use Caution Dear experts, For our study, we are planning on combining two different datasets to examine cortical thickness. There is a slight difference in the inversion time (400 vs 650) and flip angle ( 8 vs 11) between the two datasets. I know that free surfer measurements are fairly consistent across different scanner types and strengths, but do you know if slight differences in mri sequence parameters have an affect on cortical thickness? I was planning on adding it as a covariate in our analysis just in case. Thank you! Arsenije

2 1

Subcortical divide parcellation
by WANG Huifang 10 Jan '19

10 Jan '19

External Email - Use Caution Dear freesurfer experts, I would like to do subcortical divide parcellation, such as the hippocampus. By my understanding in freesurfer, the cortical parcellation can be saved as vertices but subcortical parcellation is only saved as volumes. There are a few ways I can do the cortical divide parcellation, seems do not fit for subcortical parcellation, such as: mris_divide_parcellation. Can this function also do for the subcortical regions? Is any other suggestion for this-subcortical divide parcellation? Thank you so much, Huifang

2 3

Pial surface error (failing dura removal)
by Rusche, Johann 10 Jan '19

10 Jan '19

Dear Freesurfers, I have been processing my T1 dataset through the longitudinal pipeline with the -3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large areas of dura are being included in the pial surface. Both gcut and adjustment of watershed parameters (down to 5) did not bring significant improvements. I understand intensity characteristics are very similar for GM and dura. However, I wonder whether you can recommend a more elegant solution than painfully recon-editing all brainmasks by hand. Attached is a screenshot depicting the issue with and without gcut. I am using stable v6.0. Thanks for your time! Best, Johann __________________ Johann Rusche Graduate Research Student, Lazar Lab Department of Psychiatry – Neurosciences Massachusetts General Hospital

2 3

Help with Reviewer Comment
by Shane Schofield 10 Jan '19

10 Jan '19

External Email - Use Caution Hi Freesurfer A reviewer asked whether there are concerns about whether Freesurfer may obtain accurate cortical thickness data in people with developmental conditions - the main focus in my study. I did a search and could not find any validation studies in these cohorts. Any idea? Thanks a lot. Regards,Shane

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