Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Fwd: OHBM 2015 Call for Council Nominations
by Douglas N Greve 01 Oct '14

01 Oct '14

FYI -------- Original Message -------- Subject: OHBM 2015 Call for Council Nominations Date: Wed, 01 Oct 2014 15:28:53 -0500 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu <mailto:info@humanbrainmapping.org> Dear OHBM Member: Strong leadership is the key component to setting and accomplishing OHBM’s strategic goals and in anticipating future needs. The OHBM Nominating Committee will continue to work diligently to develop a slate of candidates for election on the Executive Council, but *we need your participation now in identifying candidates.* The Nominating Committee is pleased to invite OHBM members to nominate individuals to serve on the OHBM Executive Council. Open positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program Chair-Elect and Education Chair-Elect. The term of service begins in June 2015, and each term is for three years. Please make your nominations by completing the *Call for Nominations* <http://www.humanbrainmapping.org/i4a/forms/index.cfm?id=25> form no later than *Friday, November 14^th at* *11:59 PM US CST*. Self-nominations are welcome and encouraged. The OHBM By-Laws <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3292>, Article 5 provides the framework and process for the election of new Council members. *OHBM Nominating Committee:* Doug Greve, Secretary Tonya White, Secretary-Elect Simon Eickhoff, Past Secretary Karen Berman, Chair Karl Zilles, Chair-Elect Steve Smith, Past Chair You must, when making your nominations, specify a position you want the person to fill (Chair Elect, Treasurer Elect, Secretary Elect, Program Chair Elect, Education Chair-Elect). Please check with this person before you make the nomination to be sure they would be interested in serving. Once the final slate is prepared and distributed, members will be able to see a brief bio on each candidate and vote online via the OHBM website. The results of these elections will be announced during the Town Hall Meeting, Wednesday, June 17, 2015, during the OHBM Annual Meeting in Honolulu, Hawaii. All candidates identified on the ballot will be informed of the results prior to the Annual Meeting. *Current 2014-2015 OHBM Council:* * Karen Berman, Chair * Karl Zilles, Chair-Elect * Steve Smith, Past Chair * Jeanette Mumford, Treasurer * Kevin Murphy, Treasurer-Elect * Jia-Hong Gao, Past Treasurer * Doug Greve, Secretary * Tonya White, Secretary-Elect * Simon Eickhoff, Past Secretary * Jack Van Horn, Program Chair * Andreas Kleinschmidt, Program Chair-Elect * Pedro Valdes Sosa, Past Program Chair * Niko Kriegeskorte, Chair Education Subcommittee * Martin Lindquist, Chair-Elect Education Subcommittee Councilors are not eligible for re-election for three years after serving one term. Individuals who are currently ineligible as nominees due to service on Council within the past 3 years are listed below. *Not Eligible Until 2017/2018* * Susan Bookheimer, 2013-2014 Chair * Julian Doyon, 2013-2014 Treasurer * Thomas Nichols, 2013-2014 Secretary * Peter Bandettini, 2013-2014 Program Chair * Klaas Enno Stephan, 2013-2014 Education Chair *Not Eligible Until 2016/2017* * Maurizio Corbetta, 2011-2012 Chair * Christian Beckmann, 2011-2012 Treasurer * Hugh Garavan, 2011-2012 Secretary * Katrin Amunts, 2011-2012 Program Chair * Michael Beauchamp, 2011-2012 Education Chair We look forward to your involvement in the identification and election of your association’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) ------------------------------------------------------------------------ *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>.

1 0

Boston FreeSurfer Course
by Allison Stevens 01 Oct '14

01 Oct '14

Hello everyone, The next FreeSurfer Course will be held October 27th-29th at the Martinos Center in Charlestown, Massachusetts. Registration for the course is now open: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription **Important: If we do not get at least 40 registrants for this course, we will have to cancel it. Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. This course will contain a Diffusion analysis component. fMRI analysis will *not* be taught. Registration is first-come, first-serve. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an *email confirmation* that you successfully registered for the course. Allison Stevens Lab Manager FreeSurfer Development Team Laboratory for Computational Neuroimaging Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129

1 1

normalizing activation maps
by lorenzo pasquini 01 Oct '14

01 Oct '14

Dear Freesurfers, I have a question regarding normalization of functional activation maps. Let us assume I have functional activation maps on a vertex space (e.g. mgh files reflecting degree centrality, which do not need previous normalization of functional data). After resampling activation maps into individual vertex space (bbregister and vol2surf), I want to investigate if any differences across two groups are detectable regarding this activation maps. Which pipeline/command/stream is better to use for first normalize the activation maps into a common template and then create an output that can be implemented into mri_glmfit ? Should fsfast be used? Or is mri_surf2surf better? Thanks a lot, Lorenzo

2 1

tkmedit 'no license' error
by Smith, Michael 01 Oct '14

01 Oct '14

Hello Freesurfer Team! I’ve been having an issue using the tkmedit function in freesurfer. I get the following error: ERROR: FreeSurfer license file /Users/smig9x/Applications/freesurfer//.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. However, I do in fact have both a license.txt and LICENSE file in my freesurfer home directory. Why am I still receiving this error message? Thanks in advance for the help! Best, Michael S.

2 4

display thickness map in freeview
by Harms, Michael 01 Oct '14

01 Oct '14

2 1

Two questions: 1. Regarding ASEG and reduced FOV; 2. Regarding ventral diencephalon contents
by Matthew Sacchet 01 Oct '14

01 Oct '14

Hi all, I was hoping to gain insight regarding two questions associated with the use of FreeSurfer's aseg (Fischl, Neuron 2002): 1. I have been using aseg to assess volumetric differences across populations. For one of our individuals a portion of the right hemisphere was not fully collected. The entirety of the subcortical structures we are interested in were collected (I've attached an image to this message, not sure if images propagate to the list...). Will the lack of whole-brain coverage bias the segmentation for the hemisphere that was not fully collected? I'm assuming that the fully covered hemisphere's data will be ok. 2. Regarding the "ventral diencephalon" region that is segmented using aseg, is there a 'gold standard' citation that describes what anatomical structures are included in this region? Previously on the FreeSurfer list serve there was mention from Anderson Winkler that the VD includes "The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra)", but no citation was given. In Glahn et al. (Biological Psychiatry 2012 71, 6-14) it is stated that the VD mostly includes the hypothalamus, but again, as far as I can tell, a citation is not offered. Any help would be appreciated, thank you, Matthew

2 2

create a label file in tkmedit
by Adam, Ruth 01 Oct '14

01 Oct '14

Hi all, I am creating a label file using the select voxels tool in TkMedit. However this doesn't work properly with e.g. all saved vertex IDs are set to -1. Example file: #!ascii label ….. , from subject ….. vox2ras=TkReg 19 -1 -40.000 52.000 21.000 110.0000000000 -1 -39.000 52.000 21.000 110.0000000000 -1 -38.000 52.000 21.000 110.0000000000 -1 -37.000 52.000 21.000 110.0000000000 -1 -37.000 52.000 19.000 110.0000000000 -1 -37.000 52.000 17.000 102.0000000000 -1 -38.000 52.000 17.000 108.0000000000 -1 -39.000 52.000 18.000 110.0000000000 -1 -39.000 52.000 19.000 110.0000000000 -1 -39.000 52.000 20.000 110.0000000000 -1 -38.000 52.000 20.000 110.0000000000 -1 -38.000 52.000 19.000 110.0000000000 -1 -38.000 52.000 23.000 110.0000000000 -1 -38.000 52.000 22.000 110.0000000000 -1 -37.000 52.000 22.000 109.0000000000 -1 -37.000 52.000 20.000 110.0000000000 -1 -39.000 52.000 22.000 110.0000000000 -1 -39.000 52.000 24.000 108.0000000000 -1 -39.000 52.000 23.000 110.0000000000 Any ideas how this can be solved? Many thanks in advance! Best, ruthi

2 1

make movies of non eeg/meg temporal data ?
by Gregory Kirk 01 Oct '14

01 Oct '14

I would like to make a movie of the temporal evolution of data on the cortical surface from something im doing. similar to what mne_make_movie does, but it's not eeg/meg data. is there a way to make and display movies of data in tksurfer or freeview ? or i guess i could `trick` mne and display my data in the mne package viewer ? any ideas on what is the easiest/best way to skin this cat ? thanks Greg

3 2

Problems with manual grey matter editing
by Zamroziewicz, Marta Karolina 01 Oct '14

01 Oct '14

Hello, We have some reconstructions with a significant amount of grey matter excluded in the temporal cortex and are having problems using manual voxel editing to fix this. Our correction process for brain tissue that wasn’t included in the pial/white matter outlines has been as follows: 1. When white matter is excluded from the white matter outline, we’ve used control points to identify missed white matter. We then re-run using the following command: recon-all -autorecon2-cp -autorecon3 -subjid <SUB_ID>. 2. When grey matter is excluded from the pial outline, we first make sure that white matter is outlined appropriately. If adding control points doesn’t fix the grey matter problem, we manually add grey matter voxels to the brainmask volume using the voxel edit tool. We then re-run using the following command: recon-all -autorecon-pial -subjid <SUB_ID>. In some cases (especially in the temporal cortex), the new reconstructions don’t incorporate the manually added grey matter voxels into the pial outline. I’ve attached an image of a subject who didn’t have white matter problems but did have excluded grey matter in the temporal cortex. We reran this subject using the recon-all -autorecon-pial -subjid <SUB_ID> command and the newly added grey matter voxels weren’t included in the new pial outline. Is there a way to address this problem? Thank you very much for your time! Marta _________________________________ Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2(a)illinois.edu<mailto:mzamro2@illinois.edu> 815-980-3882 _________________________________ [cid:5F7AEAD8-4EA8-49CB-A4C2-7502236F5F01@beckman.uiuc.edu]

2 1

Can't set values in tksurfer "Phase encoded data display" window
by Andre Salles Cunha Peres 30 Sep '14

30 Sep '14

Hello, I'm working with retinotopic maps, and how my experiments was with polar stimulus I want to change the angle cycles to 2 in tksurfer, however it is impossible to change the values in the "Phase encoded data display" window (View>Configure>Phase encoded data display). I can select the text in the edit text, however when I type the new value, nothing happens. Could someone help me? Thanks, Andre Salles Cunha Peres Federal University of Rio Grande do Norte Brain Institute http://www.neuro.ufrn.br/?lang=en Av. Nascimento de Castro, 2155 59056-450 - Natal / RN

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