Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

mris_make_surfaces -first_wm_peak - change of behavior in V6beta version
by Antonin Skoch 07 Jan '17

07 Jan '17

Dear experts, I have noticed changes in behavior of mris_make_surfaces with -first_wm_peak option in V6beta version after 20th December 2016. (This option is used in HCP pipelines in FreeSurferHiResWhite.sh script). This new version or mris_make_surfaces produces white surfaces much internally (i.e. away from pial surface) than version before 20th December which appeared to me more anatomically correct. See the screenshot (yellow surface is white surface before 20th December, red surface is white surface after 20th December, it seems to be placed too internally wrt white/gray interface. The commit from 20th December relating to this modification states that there is change of -first_wm_peak behaviour to look for peaks in 2nd derivative. Could you please comment on? Regards, Antonin Skoch

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Getting aparc+aseg without running the whole recon-all process
by Halász László 07 Jan '17

07 Jan '17

Dear fellow Freesurfer users, I just wanted to ask whether there is simpler and shorter way for getting aparc+aseg without running the whole recon-all process? I'm not familiar with all the steps that run during recon-all. If there is a shorter way that is not so time consuming, please guide me through the required steps. Thank you for your help, László Halász

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change the background color of screenshot of Freeview
by Hao wen 07 Jan '17

07 Jan '17

Hi, everyone: I have a simple question, i want to save the screenshot in Freeview, but the default background is black, I can not find the option to change the black background to be white, do you have any idea??? Here is the default output screenshot in Freeview: [cid:0d359a84-c5fa-41b6-aac0-1715cf7bcfc7] Can you give me any clue?? Change the background from preference does not work.. Thanks in advance Hao

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freeview error (libpng12.so.0) on Ubuntu
by Jeffrey Crawford 06 Jan '17

06 Jan '17

Hello all! I know there are issues with freeview use on Ubuntu, but I hit a wall in fixing them. I am currently getting this error when typing "freeview" into the command prompt: "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" My current version of Freesurfer is: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a.tar.gz >From the research I did online, first, I used these commands from this mail archive https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43219.html then installed what was supposed to fix something similar from the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/Download by doing "sudo apt-get install libjpeg62" Now I have been trying to install "libpng12.so.0" or some variation on that, but linux does not seem to be able to find it. Any help? -Jeff

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Tracula, adapt Freesurfer structure into other stucture hieraachy
by Hao wen 06 Jan '17

06 Jan '17

Hello, Tracula expert: I am here again, I want to know right now, the 5.3 version tracula seems to only support Freesurfer recon-alled structure, so in the config file, it works like this: set subjlist = ( sub-PREVDEMALS0010001BE_ses-M0 ) because i want to apply tracula also into my own recon-alled structure, lets call it CAPS, and I define the sublist like this: set subjlist = ( sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0 ) So this gives me some error when running trac-all -priors: #@# Priors Thu Jan 5 15:19:27 CET 2017 Standard error: /tmp/subj33.sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0.3193.txt: No such file or directory. Return code: 1 Interface CommandLine failed to run. Interface Function failed to run. So my question is trac-all is only compatible with FS structure??? if I want to adapt it to other hierarchy, i have to touch the trac-all.tcsh source code, right?? Thanks in advance Hao

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minor edits to aseg lead to exist with errors in about 25% of my scans
by Lucette Cysique 06 Jan '17

06 Jan '17

Dear Bruce Many thanks We are doing the aseg edits in Freeview. Is that an issue? I will use the command line you sent Many thanks Lucette ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Friday, January 6, 2017 4:00:04 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 155, Issue 8 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. V6 beta freeview - stopped loading remaining files when one is missing (Antonin Skoch) 2. freeview V6beta - reposition surface option (Antonin Skoch) 3. Re: mri_convert error message (Bruce Fischl) 4. Re: V6 beta freeview - stopped loading remaining files when one is missing (Ruopeng Wang) 5. Re: 6.0.0 release (Tobias Granberg) 6. Problem with freeview (Jennifer Szeto) 7. Re: minor edits to aseg lead to exist with errors in about 25% of my scans (Lucette Cysique) 8. Re: minor edits to aseg lead to exist with errors in about 25% of my scans (Bruce Fischl) 9. Re: Problem with freeview (Ruopeng Wang) 10. Re: Problem with freeview (Jennifer Szeto) 11. Postdoctoral Fellow in Machine Learning in Neuroimaging (Thomas Yeo) 12. Postdoctoral fellow in mental disorder subtypes (Thomas Yeo) 13. Fwd: REMINDER: OHBM 2017 Call For Council Nominations (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 4 Jan 2017 21:38:53 +0100 From: Antonin Skoch <ansk(a)ikem.cz> Subject: [Freesurfer] V6 beta freeview - stopped loading remaining files when one is missing To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1798454155-32478(a)posta.medicon.cz> Content-Type: text/plain; charset="utf-8" Dear experts, with V6 beta version of freeview I encountered, that when some input file specified in command line is missing, the loading of remaining files is stopped. This was not the case with 5.3 version. I found this feature handy. Do you think that it would be good to implement this behavior also for V6 version of freeview? Regards, Antonin Skoch

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recon-all in stages with T2pial
by miracle ozzoude 06 Jan '17

06 Jan '17

Hello Freesurfer, I was trying to run recon-all in stages (autorecon1, autorecon-2 and autorecon3) with T2. First, I ran autorecon1 with T2 (recon-all -autorecon1 -i input_volume -T2 /T2_volume -T2pial -s ) and i got an error (MRISread (........./surf/lh.white): could not open file Loading mov Projecting LH Surfs Loading lh.white surf No such file or directory. When can I use the -T2 -T2pial command? Also, which set of recon-all scripts is correct? recon-all -autorecon1 -i /input_volume -s recon-all -autorecon2 -T2 /T2_volume T2pial -s recon-all -autorecon3 -T2 /T2_volume T2pial -s OR recon-all -autorecon1 -i /input_volume -s recon-all -autorecon2 -s recon-all -autorecon3 -T2 /T2_volume T2pial -s Thank you Best, Paul

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Computer Hardware Requirements (iMAC)
by Alexandre Boutet 05 Jan '17

05 Jan '17

Dear all, I apologize if a similar question was asked approximately 6 months ago but I just want to double check the information validated by a single person previously. I'm thinking about starting a cortical thickness analysis as well as segmentation analysis. Therefore I want to buy a new iMAC 21.5" with the following specs: - 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3 GHz) - 16 GB 1867 MHz LPDDR3 RAM (on-board) - Intel Iris Pro Graphics 6200 Would anyone confirm that it supports Free Surfer analysis, particularly the graphic card included? Thank you for your help. Best regards, Alexandre

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Fwd: REMINDER: OHBM 2017 Call For Council Nominations
by Douglas N Greve 05 Jan '17

05 Jan '17

-------- Forwarded Message -------- Subject: REMINDER: OHBM 2017 Call For Council Nominations Date: Thu, 05 Jan 2017 05:31:34 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Dear OHBM Member: The OHBM Nominating Committee is pleased to invite current 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. We are seeking individuals with proven scientific leadership expertise, strategic thinking and planning skills, strong problem solving skills, results oriented, visionary, strong ethics, have a global perspective and are available to participate and commit time. A knowledge of OHBM activities and consistent attendance at the Annual Meeting is desired. The Council is committed to supporting a diverse membership and strongly encourages nominations from women, minorities, and members of other underrepresented groups. 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 leadership candidates.* The term of service begins in June 2017, and each term is for three years. *Remember *to make your nominations by completing the *Call for Nominations* <https://www.humanbrainmapping.org/i4a/forms/index.cfm?id=97> form no later than *Wednesday, January 11^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:* Tor Wager, Secretary Christian Grefkes, Secretary-Elect Tonya White, Past Secretary Alan Evans, Chair Bernard Mazoyer, Chair-Elect Karl Zilles, 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 29, 2017, during the OHBM Annual Meeting in Vancouver, Canada. All candidates identified on the ballot will be informed of the results prior to the Annual Meeting. Councilors are not eligible for re-election for any council position 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. Current 2016-2017 OHBM Council. <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3313> *Not Eligible Until 2019/2020* * Karen Berman, 2015-2016 Chair * Jeannette Mumford, 2015-2016 Treasurer * Doug Greve, 2015-2016 Secretary * Jack Van Horn, 2015-2016 Program Chair * Niko Kriegeskorte, 2015-2016 Education Chair *Not Eligible Until 2018/2019* * Steve Smith, 2014-2015 Chair * Jia-Hong Gao, 2014-2015 Treasurer * Simon Eickhoff, 2014-2015 Secretary * Pedro Valdes Sosa, 2014-2015 Program 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>.

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Postdoctoral fellow in mental disorder subtypes
by Thomas Yeo 04 Jan '17

04 Jan '17

Dear All, I am looking for a neuroscience/psychology postdoc to apply machine learning algorithms (possibly developed in our lab) to discover and understand mental disorder subtypes from existing large-scale public databases. See recent example from our lab (http://www.pnas.org/content/113/42/E6535) Experience with psychiatric disorders (especially ASD and ADHD) is a plus, but not required. Other details below. Regards, Thomas Requirements: Ph.D. in neuroscience, psychology or related fields. The successful applicant will work with an interdisciplinary team of computer scientists and neuroscientists. Programming experience is required. He or she does NOT need to code a new algorithm, but must be able to apply existing code (or modify existing code) for his or her project. Research Webpage: https://sites.google.com/site/yeoyeo02/home Compensation: Competitive and commensurate with experience Attraction: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Contact: Email BT Thomas Yeo (ythomas(a)csail.mit.edu) with your CV. Deadline: Whenever the position is filled.

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Freesurfer January 2017