Freesurfer

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30088 discussions

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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using "label" flag w tksurfer
by Justin Baker 26 Apr '12

26 Apr '12

I've ported a tksurfer call from one system (NCF, where it was working) to another (MGH) and now the "label" argument is no longer recognized. Here is the command: tksurfer fsaverage5 lh inflated -o test.nii.gz -fthresh 3 -fmid 4.301 -fslope 1 -colscalebarflag 1 -label lh.17Networks_LH_ContA_Cinga.label -labels-under -tcl tksurfer_Taplin.tcl Can someone point me to the correct version of tksurfer? Thanks Justin

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5.1.0 volume analysis in native space
by Maya Rosen 26 Apr '12

26 Apr '12

Hi all, In v5.1.0 is there a way to do a volume analysis in native space? I know when you do mkanalysis for the surface you can use -surface self. But for the volume analysis the only flag I see is -mni305. Is there some way to give it a native space flag for the volume? Thanks! Maya

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Re: [Freesurfer] your insight: parameter definition and --tnullmin necessary?
by Betina Ip 26 Apr '12

26 Apr '12

Dear Doug, Thanks for your reply. I will compare conditions against the NULL, but the ultimate aim is to compare conditions against each other. The effect I am looking for will be very small, so I am trying to make sure I optimise the design- I really appreciate your insight. Miezin et al., 2000 NeuroImage showed that presenting flashing chequer boards with short ITI (min=2,5, mean=5s, TR=2.5 for events of 1.5 duration) resulted in highest power (mean z-score) for responses in the visual cortex compared to longer ITI. This is mainly due to the greater amount of trials shown per condition. They only used one stimulus condition and compared it to the NULL (consistent with scenario described in your point 2), however my aim is to compare different conditions against each other. I am concerned that the reduction in amplitude of closely spaced trials will affect the between-condition comparison. If the second of two closely spaced trials will have a reduced amplitude (your point 1) - and it is the amplitude between conditions I am interested, I'd be wiping out my effect of interest. If this is the case, introducing ITIs between each trial to bring back the amplitude of the second (and subsequent trials) would be better for between condition comparisons. Does this sound right? Many thanks for your patience in explaining. Betina On 04/24/2012 07:34 AM, Betina Ip wrote: > Dear Doug, > > Thank you for your excellent answers, they are very helpful. Please > allow me to summarise and ask for additional clarification: > > 1) The main problem I'd like to solve is, as you spotted, whether the > sequence will have required power to detect and effect (if there is > one!). So, please disagree with me if this is incorrect, but one way > to evaluate the potential of the sequence in terms of detecting an > effect would be to plug the condition files directly into a Fsl FEAT > analysis design matrix (FEAT>Stats>Full Model Setup> Efficiency), > which would come out with an efficiency/estimability % to detect a > statistically significant effect for a given comparison. The lower the > effect required, the more efficient the design. yes, that's fine. You'll have to enter a guess as to the level of the noise and the size of the effect. > > 2) The second question is related to spacing of NULL trials. I would > like to first run a univariate analysis and then run a multivariate > analysis. You mentioned NULL trials would be 'helpful'- could you > please clarify whether you mean having ANY null trials or having null > trials between EACH trial would be helpful? There are two answers to this. (1) The point I was trying make below is that two closely space non-null trials will result in a smaller amplitude for the 2nd. Putting a null between them helps to bring back the amplitude of the 2nd. For this you would need nulls between each event. (2) If you have a hypothesis in which you compare a condition against the null, then you need about as many null trials as you have any other condition and you don't necessarily need nulls between each condition (sounds like this is already the case). > > My current design is allocating as much total null time as for any > other condition (as recommended in freesurver list). This means that I > do have some NULL trials, and they are randomly inserted in the > sequence. However, most trials have no ITI between them. If I did > force ITIs between EACH trial I would have to decrease number of > trials for each condition type, which could lower the design efficiency. > > IF the problem of having carry-over effects of closely very spaced > trials (i.e. majority of trials with no separation between trials) > could be alleviated by rigorous first order counter-balancing within > Optseq2 using the --focb option, is it necessary at all to add a null > trial between EACH trial into the design? The carry over is not the problem, it is the reduction in amplitude for the 2nd of closely spaced trials. doug > > Thanks for your clarification. > > Best, > > Betina > > Hi Betina, see answers below > doug > > On 04/23/2012 12:04 PM, Betina Ip wrote: > >/ Dear Freesurfer list, > />/ > />/ I am using optseq2 for the first time and wanted to check with you > whether my protocol makes sense, many thanks in advance for your insight. > />/ > />/ 1) I start by choosing the maximum scan duration equalling ~30 min: > /You might want to break this up into shorter chunks. It's totally up to > you, you just don't need to have everything in a single run. > >/ 2) set the psd window so it can capture the entire waveform of a 4 second > >event > />/ 3) select equal amounts of trials for each of the 4 event types, I > played around with it and 80 trials give me the greatest efficiency (2.72) > and variance reduction factor average (54.37). Are these values acceptable? > They are the best I could get tweaking the number of trials. > /You can't tell whether a VRF of 54 is good enough. You are asking a > question about the power of your experiment, which optseq can't answer. > If you don't have an effect, then no number of trials or efficiency will > be good enough. Having said that, I usually shoot for a VRF of between > 20 and 40, but that's just a rule of thumb. > >/ > />/ The command is here: > />/ > />/ ./optseq2 --ntp 440 --tr 4 --psdwin 0 20 \ > />/ --ev evt1 4 80 \ > />/ --ev evt2 4 80 \ > />/ --ev evt3 4 80 \ > />/ --ev evt4 4 80 \ > />/ --nkeep 3 \ > />/ --o gfatrial \ > />/ --focb 10 \ > />/ --nsearch 10000 > />/ > />/ A sample trial list is here: > />/ > />/ 0.0000 2 4.000 1.0000 evt2 > />/ 4.0000 4 4.000 1.0000 evt4 > />/ 8.0000 0 4.000 1.0000 NULL > />/ 12.0000 3 4.000 1.0000 evt3 > />/ 16.0000 3 4.000 1.0000 evt3 > />/ 20.0000 2 4.000 1.0000 evt2 > />/ … > />/ > />/ The other question I had concerns the position of null trials. Many > trials are not separated by a NULL event, however studies of rapid > event-related designs to report a minimum ITI, in this case the minimum seems > to be 0? To assess the effect of forcing a minimum ITI on the sequence, I > have run the search defining the --tnullmin to 4 sec (equal to 1 TR) however > efficiency and VRFAvg drop to .79 and 16.07, obviously due to trade of > between ntp and ntrials (ntp=440, ntrials=62). > />/ > />/ Are NULL trials between each event required at all if a standard FIR is > used for the analysis? My aim is to first apply a univariate BOLD-analysis > and subsequently a multivariate analysis to the dataset. Thanks for > clarifying. > /They are not strictly necessary, however, they may be helpful. If you > really don't want them as part of your design (eg, it would interfere > with the psychology), then don't use them but make sure to optimize the > FOCB more (I usually use 100 regardless). The disadvantage of not having > the nulls is that there will probably be some non-linearity in that the > second of two closely spaced trials will have a lower amplitude than if > it occurred in isolation. This will hurt your power and might cause a > false difference between conditions if they are not well counter-balanced. > doug > >/ > />/ Betina > />/ _______________________________________________ > />/ Freesurfer mailing list > />/ Freesurfer at nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > />/ https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > />/ > />/ > / > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve at nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop:www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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.

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