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30088 discussions

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*

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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

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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

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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

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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

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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

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segmentation problem
by Manuela Costa 10 Jan '19

10 Jan '19

External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation. Unfortunately, this subject has a large lesion in the right hemisphere. Looking at the aseg, the segmentation of the bilateral amygdala are fine, but the right hippocampus becomes incorrectly segmented towards the posterior end (shown in the attached images). Is there any way that this can be corrected, manually or otherwise? Will there be further problems down the line when we proceed with the subfield segmentation? We are running freesurfer-linux-centos6_x86_64-dev-20181121-910b841. Thanks in advance! Regards, Manuela -- Manuela Costa, PhD Cognitive Neuroscientist Lab. for Clinical Neuroscience,CTB, Madrid <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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problem with contrast in 1st-level analysis
by xi star 10 Jan '19

10 Jan '19

External Email - Use Caution Hi! FS Experts! In the fMRI experiment, there are 2 conditions: 1# 3D picture 2# zero disparity picture interleaved with fixation block (0). To compare 3D-vs-zero disparity, I used command: mkcontrast-sess -a 1 -c 2 -nosumconds but the results showed more activation then expected. To find the problem, I compared 3D-vs-fix (-a 1 -c 0), the result shows the same as 3D-vs-zero disparity. My question is: why the two contrast ( [1 0; 0 -1] and [1 0] ) came to the same result? How can I compared the two conditions? Thanks a lot ! Yours, Star

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freeview.bin: Fatal IO error: client killed
by 이충섭 10 Jan '19

10 Jan '19

External Email - Use Caution Hello Freesurfer developers, First, the recon-all command was completed without errors. However, the following command results in the same error as the mail subject . freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red If i enter only freeview, it runs without error.. Can you tell me what's wrong? Thank you. 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) platform: Ubuntu 16.04.5 LTS 3)uname -a: Linux eclgpu4 4.4.0-135-generic #161-Ubuntu SMP Mon Aug 27 10:45:01 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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Yeo labels
by Tosun, Duygu 09 Jan '19

09 Jan '19

External Email - Use Caution Is there a recon-all flag similar to -label_v1 or -ba-labels to automatically create label and stat files for Yeo network parcellations?

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