Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

T2pial and [LONG]
by Kasper Jessen 18 May '16

18 May '16

Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface. Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces? Best regards, Kasper Jessen

3 6

Same coordinates for all labels
by Nabin Koirala 18 May '16

18 May '16

Dear FS team, I am trying to find the centroid using mri_surfcluster using the following command but I am getting the same coordinate for all labels. I couldn't quiet understand what's wrong. Your suggestion would be really appreciated. NOTE: The coordinates differs for hemisphere. mri_surfcluster --in ./S/surf/rh.thickness --clabel ./S/centroid/rh.frontalpole.label --sum ./S/centroid/sum.rh.6.label --centroid --thmin 0 --hemi rh --subject S Thank you. Regards, Nabin

2 2

Question on Yeo 2015 cognitive atlas
by Josh Gray 17 May '16

17 May '16

Hello, I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website). Is there a quick way to do this? Thank you, Josh Gray -- Graduate Student Psychology Dept. - Clinical Program Experimental & Clinical Psychopharmacology Laboratory University of Georgia

2 1

Re: [Freesurfer] Freesurfer (white/grey matter changes)
by Limachia, Gaurang (NIH/NINDS) [F] 17 May '16

17 May '16

This is how the white matter changes look like after making corrections and running recon all. From: "Limachia , Gaurang (NIH/NINDS) [F]" <gaurang.limachia(a)nih.gov<mailto:gaurang.limachia@nih.gov>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, May 17, 2016 at 4:49 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Freesurfer I made the necessary changes to the white matter, and when I ran recon all the changes with the voxels showed up, but there was no change to the contour lines. In order to change the gray matter volume, I can¹t find the changes I already made on the white matter (the picture with green control points). If I am able to see the changes I made to the white matter, I can utilize the control points to modify the segmentation. Also will this impact the gray matter volume as well as per your previous response to my question. Thanks, Gaurang

2 4

Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill
by gangli 17 May '16

17 May '16

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic and critical early brain development in both health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu <https://outlook.unc.edu/owa/redir.aspx?SURL=r-ilRGXKGkv6jOyzGz3FjAPbDG9VNfM…> ). For more information, please visit: http://www.unc.edu/~gangl/contact.html <https://outlook.unc.edu/owa/redir.aspx?SURL=HcVZFV_dUot9RdWseT8XGNDO-UYKJHN…> .

1 0

wm parcellation
by Caroline Beelen 17 May '16

17 May '16

Dear FS team, Thank you for your answers before (email: WmParc). We now realize that we've formulated our question wrong, since our problem is mainly in creating the wmparc.a2009s.mgz file. We ran the following command: mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz (<subjid> was replaced by our subject and the ribbon command was set to 'noribbon' because we otherwise received the message the that the ribbon command was unknown.) If we run this command, we can extract grey matter labels with fslmaths (e.g. 11136 for the left planum temporale), but not the white matter labels we are looking for (this is 13136 for the left planum temporale). The problem seems to be in the labelling of the white matter. Many thanks. Jolijn & Caroline

2 1

Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 17 May '16

17 May '16

Hi Doug, Yes, you are correct- data I have previously processed without any problems is no longer being processed. My version of freesurfer is 5.3.0; I only downloaded it a few weeks ago so I have not changed my freesurfer version recently. Thanks! Joseph Aloi Graduate Student, MD/PhD Scholars Program Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Neurobehavioral Research Assistant, Center For Neurobehavioral Research Boys Town National Research Hospital The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

2 1

Big ventricles and recon-all error
by Kasper Jessen 17 May '16

17 May '16

Dear FreeSurfer group, I am having problems with a subject with very large ventricles. The recon-all exits with errors. Is it known issue that FreeSurfer is having difficulties with large ventricles? How can i solve this problem? I have read in another post, that the flag -bigventricles may solve the problem? Best regards, Kasper

2 3

mri_coreg !
by Elijah Mak 16 May '16

16 May '16

Hi Doug and Martin, Thanks both for your responses. I am working with PK11195, AV-1451, and PiB. In general, the standard bbregister routine with init-fsl works well for AV-1451 (adjustments needed in 30% of cases) and PiB (best performance), but it completely failed with the PK data which was acquired on the same scanner. I tried running the registration using the mean image (mri_concat --mean) but it did not help too. All that being said, mri_coreg works extremely well for the PK11195 (only 3 manual adjustments needed so far for > 50 scans), so I am very grateful for this tool :) If I want to run the analyses of the various PET data in the same study, will it be of concern that I am using a mix of boundary-based (AV and PIB) and normalised mutual information (PK)? Best Wishes, Elijah Re: [Freesurfer] mri_coreg ! <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subje…> Martin Reuter <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 16 May 2016 13:23:13 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi, just wanted to mention that the --cost NMI (normalized mutual information) and MI implementations in mri_robust_register are the same as spm_coreg and now mri_coreg (if the -nosym flag is specified in robust register, else it is registering in a symmetric midspace instead into the target space). If you have cases where robust_register fails, but the other tools work, let me know, because that could indicate a bug in my code. Thanks, Martin On 05/16/2016 03:19 PM, Douglas N Greve wrote: > It is my implementation of the spm_coreg program written by John > Ashburner using normalized mutual information. I liked the spm program > so much that I put the effort into replicating its behavior in C. My > guess is that BBR was failing because the initialization was failing. > Still I like mri_coreg for PET data because the blurriness can throw BBR > off a bit. What kind of PET data do you have? > > > On 05/16/2016 03:06 PM, Elijah Mak wrote: >> Hi Doug, >> >> I just want to say that mri_coreg worked tremendously well for the >> registration of some very blurry PET-PK data. I was not getting any >> success with bbregister and init-fsl or mri_robust_register options. >> >> How does this technique differ from the boundary-based registration? >> >> Thanks a lot. >> >> Best Wishes, >> Elijah >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

2 1

Postdoctoral position in neuroimage analysis
by Bruce Fischl 16 May '16

16 May '16

Postdoctoral Research Fellow Position Neuroimaging Analysis of Human Brain Connectivity in Dementia www.nmr.mgh.harvard.edu/working/employment#20160516 The Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging invites applications for a postdoctoral Research Fellow position at the Massachusetts General Hospital and Harvard Medical School. Funded by the BrightFocus Foundation, the project consists of human brain connectivity analysis and its application in studying Alzheimer’s disease. The appointment starts as early as September 2016, and is for two years with the possibility of a third year based on performance and the availability of funding. The project involves analyzing structural and functional brain networks through diffusion-weighted and functional MRI, and examining their relationship with different stages of dementia. In particular, we would like to identify the relative roles of direct and indirect neuronal connections. The Research Fellow will be supervised by Dr. Iman Aganj, with close collaboration with Dr. Bruce Fischl and Dr. Reisa Sperling. The candidate is required to have: · a Ph.D. in engineering, neuroscience, or a related field by the start date, · strong programming skills in MATLAB or a similar environment, and · a medical image analysis background. Familiarity and experience with any of the following will be a plus: connectomics, neuroimaging, diffusion-weighted MRI, functional MRI, graph theory, machine learning, dementia studies, mathematical modeling, Linux operating system. Interested applicants should send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: iman(a)nmr.mgh.harvard.edu

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