Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30133 discussions

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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Postdoctoral Fellow in Machine Learning in Neuroimaging
by Thomas Yeo 04 Jan '17

04 Jan '17

Dear All, I am looking to hire a postdoc to develop machine learning algorithms for large-scale publicly available MRI and behavioral data. Experience with probabilistic machine learning (aka graphical models) or deep learning is a plus. The ultimate goal is automatic scientific discovery (see recent paper from our lab: http://www.pnas.org/content/113/42/E6535) Topics are flexible, e.g., multi-modal fusion, individual-subject brain parcellation, individual subject behavior prediction, dynamic functional connectivity, meta-analysis, neural mass modeling, multi-scale neuroscience, graph theory, mental disorder subtypes, etc. Other details below. Regards, Thomas Requirements: Ph.D. in computer science, electrical engineering, statistics, computational neuroscience or related fields. The successful applicant will work with an interdisciplinary team of computer scientists and neuroscientists, and must be willing to learn some neuroscience. 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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Problem with freeview
by Jennifer Szeto 04 Jan '17

04 Jan '17

Hi Freesurfer Experts, I have installed Freesurfer5.3 and it seems to be working fine. However when i tried to load up the GLM analysis (after doing mris_preproc and mri_glmfit) results on freeview, i got the following message: "OpenGL warning: No pincher, please call crStateSetCurrentPointers () in your SPU Did not find any volume geometry information in the surface" Just wondering if anyone knows the solution to this? Thanks for your help! Jen

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minor edits to aseg lead to exist with errors in about 25% of my scans
by Lucette Cysique 04 Jan '17

04 Jan '17

Dear FS Wiki I run my scan in FS without any problem example: #@#%# recon-all-run-time-hours 8.342 recon-all -s 877 finished without error then I do some edits to the aseg in freeview edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles Once done, I re-run using recon-all -s $i -autorecon2-noaseg example: /mridata/workingdata/HIV/subjects/877 /usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all -s 877 -autorecon2-noaseg in 25% of cases, I get the following error message and the process exists example: #-------------------------------------------- #@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016 /mridata/workingdata/HIV/subjects/011/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz mri_normalize: aseg volume aseg.mgz must be conformed using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016 in the other no problem example: #@#%# recon-all-run-time-hours 1.116 recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016

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6.0.0 release
by Tobias Granberg 04 Jan '17

04 Jan '17

Dear Bruce, Doug and the rest of the team, I hope you have had a pleasant start of the new year! We have noticed that there is now a 6.0.0 RC but that the modification date changes while the file name persists. We are planning on running some processing, but it seems to be better to hold off until the stable release. Any time perspective for the release? Will the Linux version be finished before the OSX version? Thanks a lot! Best wishes, Tobias _________________________________________ Tobias Granberg, MD, PhD Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology 141 86 Stockholm, Sweden Cellular: +46 700 60 60 87

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