Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

Re: [Freesurfer] Labels for ventromedial prefrontal cortex (fwd)
by Yiyu Chou 30 Apr '12

30 Apr '12

Thanks Rahul, This is much appreciated !! Also, is there a way to generate a binary mask for MOF ? Yi-Yu ________________________________________ From: Rahul Desikan [rahuldesikan(a)gmail.com] Sent: Friday, April 27, 2012 2:22 PM To: Yiyu Chou; freesurfer(a)nmr.mgh.harvard.edu Cc: Bruce Fischl Subject: Re: [Freesurfer] Labels for ventromedial prefrontal cortex (fwd) Hi Yiyu, The closest equivalent in our cortical parcellation atlas (Desikan et al., 2006) is the medial orbitofrontal cortex label. Hope this helps, Rahul On Fri, Apr 27, 2012 at 5:11 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > > > ---------- Forwarded message ---------- > Date: Fri, 27 Apr 2012 14:04:08 -0700 > From: Yiyu Chou <yiyu.chou(a)loni.ucla.edu> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Labels for ventromedial prefrontal cortex > > > Dear FS users, > > > > I wonder if FS has labels for ventromedial prefrontal cortex. > > If not, is there an easy way to build it ? > > Thanks !! > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://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 at > http://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. > -- Rahul S. Desikan, MD, PhD Multimodal Imaging Laboratory Department of Radiology University of California, San Diego 8950 Villa La Jolla Drive, Suite C101 La Jolla, CA, USA 92037-0841 Email: rdesikan(a)ucsd.edu

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Gray matter hyperintensities and subcortical segmentation
by Julius Juurmaa 30 Apr '12

30 Apr '12

Hello! This is probably a novice question, but here goes. We are using FreeSurfer to reconstruct the brains of a number of patients, some of whom have a bilateral T1 signal hyperintensity in globus pallidus due to manganese exposure. Problem is, this hyperintensity seems to confuse FreeSurfer and the subcortical segmentation goes a bit off -- parts of the pallidum is considered cerebral white instead (see attachment; globus pallidus is violet, putamen is pink). Is there any way this could be mitigated? Thank you in advance :) -- Julius Juurmaa ut.ee/~ogion julius.juurmaa(a)ut.ee (+372) 5559 3249

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submitt job with either interactive qsub or nested qusub with PBS
by Knut J Bjuland 30 Apr '12

30 Apr '12

I have used trac-all on the cluster where I have an account. I am able to start both prep and post part as qsub process. Are there anyone who has modifed trac-all to be used with qsub in such a manner that a single node then submits jobs to other nodes? Or is there a path I should use to make trac-all work with PBS/torque. I have been able to use trac-all from the frontend of the cluster. Knut J

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MRI Position at Department of Neurology, New York University School of Medicine
by Thesen, Thomas 29 Apr '12

29 Apr '12

We are seeking a full-time postdoctoral research fellow or MRI staff physicist to help organize and support a multi-site, longitudinal MRI study in epilepsy patients and controls. Experience in multi-site MRI studies is highly desirable, and experience with multimodal MRI methods and longitudinal analysis would be advantageous. The position requires sequence set-up, quality control at multiple sites and at the home site in New York, and data analysis,. Minimal traveling is required. Opportunities exist for qualified candidates to pursue their own research within the larger study. A Master degree or Ph.D. and relevant experience in biomedical field, physics, engineering or computer science is required, as is programming experience in Matlab and Unix scripting. The position is available for 4 years and includes excellent benefits. Start date can be immediately or later upon agreement. Please direct all inquiries and applications with resume and cover letter to: Thomas Thesen, Ph.D. thomas.thesen(a)med.nyu.edu<mailto:thomas.thesen@med.nyu.edu> and Ruben Kuzniecky, M.D. ruben.kuzniecky(a)med.nyu.edu<mailto:ruben.kuzniecky@med.nyu.edu>

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Freesurfer Team - Job Opening - Software Engineer - Build/Test/Release/Maintenance/Support
by Nick Schmansky 29 Apr '12

29 Apr '12

We have an opening on the Freesurfer team for a Software Engineer. The responsibilities of this position and contact information are described on our wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/SoftwareEngineer The Freesurfer team

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[Release] - iSurf BrainView 4.0.5
by Pedro Paulo de Magalhães Oliveira Junior 28 Apr '12

28 Apr '12

Today it was released the version 4.0.5 of iSurf Brainview, it's a major redesign version release for IPad, IPhone and IPod Touch. The UI has been redesigned to be more compliant to the Apple Human Interface Guidelines. As usual suggestions and feedback are welcome. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… Note: A version for Windows Phone 7.5 (Nokia Lumia 900, 800, 710, etc) is under development. --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Labels for ventromedial prefrontal cortex
by Yiyu Chou 27 Apr '12

27 Apr '12

Dear FS users, I wonder if FS has labels for ventromedial prefrontal cortex. If not, is there an easy way to build it ? Thanks !!

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Trac-all on a cluster with PBS/torque
by Knut J Bjuland 27 Apr '12

27 Apr '12

Hi I am trying to run Trac-all on a cluster with PBS/torque. The trac-all scripts was modified to run with qsub, but the second stage in Trac-all crash without getting finished. This is tested with the tutorial data. I am enclosing the modified trac-all script. Best regard Knut J Bjuland NTNU

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Announcing Release of PySurfer 0.3
by Michael Waskom 26 Apr '12

26 Apr '12

Dear All, We are pleased to announce the 0.3 release of PySurfer, a Python-based package for visualizing Freesurfer data. This release includes bugfixes and quite a few enhancements, including: - Tools for reading and manipulating MEG data from MNE (thanks to work from Martin Luessi and Alex Gramfort) - The ability to visualize 4D (containing a dimension for time, etc.) data, with a lightweight GUI interface - A convenience function to project volume data in one step (currently a wrapper around mri_vol2surf) - Increased flexibility in controlling the appearance of overlay data, labels, foci, and the scene itself - Five new example scripts, with additions to existing scripts, demonstrating these enhancements - A variety of minor improvements here and there Please see our website (http://pysurfer.github.com/) for information on installation, documentation, and the example gallery. We hope you find it useful in your research! Michael Waskom and the Nipy team

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Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29
by Andrew C Yourich 26 Apr '12

26 Apr '12

I've replaced my old mris_expand file with the one downloaded from the link below, and now it is working perfectly. Thank you so much to all of you who helped me resolve this issue. I really appreciate it. - Andrew ________________________________________ From: Nick Schmansky [nicks(a)nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2012 10:18 AM To: Andrew C Yourich Cc: Bruce Fischl; gramfort(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29 i've posted a build for the mac here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-int… n. On Wed, 2012-04-25 at 15:02 +0000, Andrew C Yourich wrote: > If you all have a fixed binary for a Mac Pro running Mac OS 10.6.8 that you would be able to forward me, I would greatly appreciate it. > > Thanks, > Andrew > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Wednesday, April 25, 2012 8:56 AM > To: Alexandre Gramfort > Cc: Andrew C Yourich; Robert C Knowlton; freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 > > thanks Alex. > > If anyone needs a fix before the next release let us know what > hardware/software version you are running and we'll send you a binary > > cheers > Bruce > > On > Wed, 25 Apr 2012, Alexandre Gramfort wrote: > > > hi all, > > > > @bruce : I've just given a try your own binaries in > > > > ~fischl/dev/freesurfer/bin/ > > > > and it worked fine. It looks like a bug has been fixed since the last > > stable release. > > > > Alex > > > > On Tue, Apr 24, 2012 at 10:44 PM, Andrew C Yourich <ayourich(a)uab.edu> wrote: > >> Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well. > >> > >> Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not. > >> > >> Any other suggestions you all have would be appreciated. > >> > >> Thanks, > >> Andrew > >> ________________________________________ > >> From: Alexandre Gramfort [gramfort(a)nmr.mgh.harvard.edu] > >> Sent: Tuesday, April 24, 2012 3:24 PM > >> To: Andrew C Yourich > >> Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29 > >> > >> hi, > >> > >> have you fixed your problem? I still don't manage to make it work? > >> > >> thanks > >> Alex > >> > >> ---------- Forwarded message ---------- > >> From: Alexandre Gramfort <gramfort(a)nmr.mgh.harvard.edu> > >> Date: Mon, Apr 23, 2012 at 7:10 PM > >> Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 > >> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>, ayourich(a)uab.edu, > >> Krish Subramaniam <krish(a)nmr.mgh.harvard.edu>, Ruopeng Wang > >> <rpwang(a)nmr.mgh.harvard.edu> > >> > >> > >>> not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can > >>> answer. > >> > >> could be due to my update of XCode this morning but things work fine > >> with freeview -f lh.white -v ../mri/T1.mgz > >> on my mac with lion. sorry for the noise > >> > >>> I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the > >>> surfaces somewhere I can look at them and I'll take a look > >> > >> see the files in : > >> > >> /homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded > >> > >> that's the sample data we use for MNE. > >> > >> the log: > >> > >> $ mris_expand -thickness lh.white 0.5 lh.white.expanded > >> using distance as a % of thickness > >> expanding surface lh.white by 50.0% of thickness and writing it to > >> lh.white.expanded > >> reading thickness... > >> ending sse = 4485.856144 > >> nrounds = 6 > >> writing expanded surface to lh.white.expanded... > >> writing group avg surface area 822 cm^2 into surface file > >> surface expansion took 27 minutes and 15 seconds. > >> > >> Alex > >> > >> > >> 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 at > >> http://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. > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Freesurfer April 2012