Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

recon-all error using GPU in OS X Sierra
by June Kang 17 Nov '16

17 Nov '16

Hello FreeSurfer Developers, I'm attempting to run recon-all using -use-gpu option in Mac Pro 5,1 with OS X 10.12.1.I am using GTX980 rom-flashed edition, and it supports CUDA properly with other tools.Current cuda version is 8.0, and cudadetect command works perfect. Device 0: "GeForce GTX 980" CUDA Driver Version: 8.0 CUDA Runtime Version: 5.0 CUDA Capability Major revision number: 5 CUDA Capability Minor revision number: 2 Total amount of global memory: 4294770688 bytes Number of multiprocessors: 16 Number of cores: 448 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 65536 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 2147483647 x 65535 x 65535 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 1.22 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) However, when I run recon-all -all -s DEP030 -qcache -use-gpu, I face repeatedly the error reading transform from transforms/talairach.m3zERROR: cannot find or read transforms/talairach.m3zNo such file or directory I found it might be caused since talairach.m3z couldn’t created. I also found an error above.Cuda error: MRIconvolveKernelX failed! in file 'mriconvolve_cuda.cu' in line 536 : unspecified launch failure.freeing gibbs priors...done.average std[0] = 5.0 I also attach full log file too. Thanks.

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Re: [Freesurfer] tracula reinit
by Lars M. Rimol 17 Nov '16

17 Nov '16

Hi Anastasia! That makes sense, thank you! So the question is how do I evaluate the noisiness of a path? 1) Most of my isosurfaces look a lot noisier than your example on the wiki. There's obviously no hard and fast rule here but is there any way to gauge the noisiness of a reconstructed path? And can that information be used for quality control? 2) Another source of information on outliers is the log files that are produced when running -trac-all -stat (based on the shape of the tract). It doesn't seem to flag tracts that are (almost) completely missing (which are spotted by visual inspection in Freeview) - but they may fall under the minimum threshold and therefore not be evaluated? Would you recommend automatically excluding the subjects that are flagged as outliers here? >Hi Lars - A path with fewer control points will generally be smoother. So >if the tract is pretty much a straight line, you might get a noisier >result if you increase the number of control points. But if the tract is >more convoluted than a straight line, then you need more control points to >define it accurately. So it's hard to predict the result of increasing the >control points in general, it depends on the specific case. >BTW, if you change the number of control points, you don't need to use the >reinit variable - that's only for rerunning with the same control points >as before. > >Best, >a.y sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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[Announcement] Freesurfer v6.0 beta release and testing
by Z K 16 Nov '16

16 Nov '16

Hello All, The Freesurfer development team seeks beta testers for the beta version of Freesurfer v6.0. This is a beta release to the Freesurfer community to help identify bug fixes and other unknown issues before the stable release of Freesurfer v6.0. PLEASE REMEMBER THAT THIS IS NOT AN "OFFICIAL" RELEASE AND CHANGES MAY BE MADE THAT WOULD REQUIRE THAT YOU REANALYZE YOUR DATA. Download and installation instructions can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall6.0-beta We ask beta testers to submit any problems or issues they may encounter to the Freesurfer support list. And follow our protocols for submitting a bug report. http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting It would also be helpful to know if the issue you encounter exists in v5.3 as well. We anticipate an approximately 2 week beta testing period. Thanks for your help, -Freesurfer Development Team

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Manual vs Automatic Cortical Thickness
by Donna Cosgrove 16 Nov '16

16 Nov '16

Hi all, I was hoping to get some advice about FS edits, namely for cortical thickness analysis. We have just under 300 subjects and have run recon-all, and extracted the outliers. I am currently visually inspecting each image slice by slice to look for any artefacts/abnormalities; however, I am wondering if it is better NOT to manually edit the images unless there is something VERY obvious and easily corrected (e.g. pial surface/skull strip included)? I am concerned about bringing subjectivity into this process by carrying out manual editing of particularly the surfaces in potentially ambiguous pial/white matter boundaries. Possibly the more minor segmentation errors made by Freesurfer are more objective through the entire dataset than my manual corrections could be? Any thoughts would be appreciated on this. Apologies if this is duplicating a previously answered query! Thank you Donna

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Freeview display problems
by Robert Kraft 16 Nov '16

16 Nov '16

I am running Freeview Version 1.0 Build May 26 2016 remotely from my Mac OS 10.11.6 with X11 forwarding. I have been using this setup for years. However, within the last wee I encountered a problem with the FreeView display. Everything works fine except that the image panes are no longer visible. I can move the mouse and see the cursors updating with correct values. I just can’t see the images. The X11 forwarding appears to be working fine for other programs. Even Freeview calls up the viewer as I already described. I suspect that something on my Mac was automatically updated but I haven’t been able to figure out what. I am hoping that someone else may have an idea of what is going on. I could restore my Mac to a previous state and see if that fixes the problem. I am hoping to take a more surgical approach. Any help or suggestions would be greatly appreciated. Bob

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'Invalid' license file
by Lee.Reid＠csiro.au 16 Nov '16

16 Nov '16

Hi, Our IT department have recently upgraded our cluster OS and now Freesurfer complains that its license is invalid. I have tried rebuilding, and acquiring a new license, but these do not fix the problem. The license file I am using works in my Ubuntu 12.04 computer - it has been copied across as a file, not via a text editor - and used to work on an older version of the same OS. Do you know of any solution to this issue? I've tried everything I have seen on the mailing list, including naming it .license and license.txt, checking for whitespace, etc. Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64). Many thanks, Lee

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Left Thalamus and Pallidum segmentation problem
by Jeffrey Crawford 16 Nov '16

16 Nov '16

Hello there! I was wondering if I could get some help on an issue I am noticing in the segmentation of the left thalamus and left Pallidum on my scans. I've included pictures of tkmedit so you can see what I mean. The tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz All of my scans have been through the entire recon-all process and , out of my sample of about 172 patients and controls, just about 29 of them show this odd segmentation on, almost always, the left hemisphere. The left thalamus seems to be over estimating the size and the pallidum is underestimating its size. I was wondering why this would be and if the community thought it would be okay to go back and manually edit the segementation to fit the subcorticals structures better? Also, since I have never done such editing, is it advisable or even possible to do so?

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Two neuroimaging post doc positions available
by Kristine Beate Walhovd 16 Nov '16

16 Nov '16

Dear all, ? two post doc positions at the Center for Lifespan Changes in Brain and Cognition at the University of Oslo, Norway, are available for excellent candidates: http://uio.easycruit.com/vacancy/1717727/65775?iso=no http://uio.easycruit.com/vacancy/1715913/65775?iso=no Best wishes, Kristine Beate Walhovd Leader of Center for Lifespan Changes in Brain and Cognition (LCBC)? Department of Psychology University of Oslo POB 1094 Blindern 0317 Oslo Norway E-mail: k.b.walhovd(a)psykologi.uio.no Phone: (+47) 22845130 Cell: (+47) 46824662

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Re: [Freesurfer] differences between OS recon all output, longitudinal data
by anonymous anonymous 15 Nov '16

15 Nov '16

Thank you so much for the extense answer! It happens that the person who analysed the first measure (of this longitudinal dataset) used two different OS (he did it in a Virtual machine on windows and a mac OS X) to speed up this step. That data has already been used in some studies. ¿So my question now would be how much does that really affect to the results? > Hi > > I am using recon-all in some longitudinal data on a ubuntu 16.04, and > using > the development version of freesurfer as I was told here, because the > other > current version doesnt work on ubuntu 16.04. > > The problem is that the first scans were probablly processed using > virtualbox in a windows and an older version of freesurfer. > > > i think I already know the answer, that I can't do this if I dont want to > bias my results. Can I? Yup. You know the answer ;) However, I did discover a way to make freesurfer 5.3 work on Ubuntu 16 by doing the following steps to install an older version of perl : 1) install perlbrew: $> sudo apt-get install perlbrew 2) use perlbrew to install perl version 5.20.3: $> perlbrew install perl-5.20.3 3) You must change the '/bin/perl' file to a link which points to the version of perl installed by perlbrew. (This technique is not the standard practice but it is the only way to get the mni tools to use the older version of perl): $> cd /bin $> sudo mv perl perl.orig (can always set back later) $> ln -s ~/perl5/perlbrew/perls/perl-5.20.3/bin/perl > > But I'm using a better computer now and I use the one with windows for > other analyses, so I wanted to know if I could install Virtual box on my > ubuntu 16.04 computer, and install the same version of linux used to > process the first measure. Should I also need to use the same version of > freesurfer? You could do that, but The Virtual Box version is not really good for processing a large number of subjects because of the limited amount of disk space on the virtual image. Its really meant more as a teaching tool for users with Windows machines. > > f the computer's specs are dfferent, does it matter? And if I assign > different cpu and ram on my virtual machine? Different specs are fine. Its the OS, OS version, and version of freesurfer that should stay the same. > > Thank you! > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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tracula missing tracts and pathstats
by Lars M. Rimol 15 Nov '16

15 Nov '16

Hi Anastasia, I have two subjects, one with a lhcab that looks ok (more or less noisy but it's there) and one with a lhcab that is almost completely missing (please see attached figures). And yet, when I look at their respective pathstats.byvoxel.txt (under dpath/lh.cab_PP_avg33_mni_bbr) I find that both have data for this tract and that the subject with a seemingly missing tract (70) has more observations. Is this a thresholding issue? Which brings me to: The default threshold in Freeview when viewing these files is 20% of the 99th percentile of the posterior probability distribution for the path, isn't it? So I was wondering how that affects the data in pathstats.byvoxel and pathstats.overall; are they also thresholded? # subjectname 17 # pathwayname lh.cab # # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 56 35 27 0.000890712 0.000603441 0.000699198 0.315126 0.00105762 0.000596839 0.000750432 0.362276 56 36 26 0.00107635 0.000545558 0.000722489 0.41169 0.00104539 0.000615595 0.000758858 0.335287 56 37 26 0.00106187 0.000590571 0.000747672 0.372333 0.00105743 0.000602726 0.000754296 0.354483 56 38 25 0.00102202 0.000600078 0.000740726 0.368605 0.00100576 0.000632157 0.000756689 0.313797 56 39 25 0.00119029 0.000522558 0.000745135 0.485075 0.00107733 0.000611676 0.00076689 0.358958 56 39 24 0.000901928 0.000700433 0.000767598 0.204508 0.0010547 0.000622021 0.000766243 0.338646 56 40 24 0.000983715 0.000610012 0.00073458 0.333454 0.00105292 0.000634273 0.00077382 0.330426 56 41 23 0.00109975 0.000657692 0.000805043 0.318553 0.00115473 0.000602686 0.000786698 0.395328 57 42 23 0.00119796 0.000512441 0.000740946 0.50737 0.00119982 0.00058122 0.000787428 0.43539 57 43 22 0.00108816 0.000588772 0.000755234 0.368538 0.00120245 0.000589771 0.000793995 0.417918 57 44 22 0.00145913 0.000457154 0.000791146 0.628211 0.00131065 0.000556036 0.00080757 0.48867 57 45 21 0.00142093 0.000463346 0.000782542 0.617307 0.0013404 0.000544065 0.000809509 0.514237 57 46 21 0.00142182 0.000445771 0.000771122 0.632204 0.00139366 0.000547482 0.000829538 0.525517 57 47 20 0.000968663 0.000475497 0.000639886 0.434747 0.001285 0.000583274 0.000817181 0.448241 58 48 19 0.00121939 0.000531887 0.000761053 0.482488 0.00133092 0.000590401 0.000837236 0.462653 58 49 19 0.00159589 0.000576742 0.000916457 0.569308 0.00136598 0.000635182 0.000878787 0.437028 58 50 19 0.00164139 0.000624262 0.000963304 0.549971 0.00138664 0.000658869 0.000901467 0.426815 58 50 18 0.00157653 0.000942457 0.00115382 0.332295 0.00137177 0.000715268 0.000934107 0.385317 58 51 18 0.00118225 0.000642473 0.0008224 0.36823 0.00118518 0.000684428 0.000851342 0.330996 58 52 18 0.00109238 0.000519084 0.000710181 0.435882 0.00107605 0.000632073 0.000780059 0.324378 58 53 18 0.00129725 0.000623659 0.000848189 0.430382 0.00108778 0.000647922 0.000794535 0.315793 # pathway end # subjectname 70 # pathwayname lh.cab # # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg 53 32 26 0.00117731 0.000928949 0.00101174 0.143923 0.00116391 0.00090839 0.000993563 0.153213 53 33 26 0.0010364 0.000859843 0.000918695 0.128905 0.00103869 0.000848443 0.000911856 0.138848 53 33 25 0.00105938 0.000877392 0.000938055 0.127225 0.00105752 0.000865256 0.000929355 0.135088 54 34 25 0.000944648 0.000719044 0.000794246 0.162868 0.000957389 0.000725472 0.000802768 0.16744 54 35 25 0.000972687 0.000738523 0.000816578 0.208351 0.000986717 0.000739063 0.000821629 0.213113 54 36 24 0.00101603 0.000621378 0.000752929 0.305637 0.0010253 0.000631396 0.000762693 0.302995 54 37 24 0.00113992 0.000642822 0.000808521 0.369124 0.0011217 0.000646204 0.000804698 0.353409 55 38 23 0.000890718 0.000584601 0.00068664 0.265622 0.000916719 0.000590972 0.000699556 0.273432 55 39 23 0.0013084 0.000657441 0.000874427 0.41632 0.00129438 0.000656492 0.000869102 0.409684 55 40 22 0.000897226 0.000549981 0.000665729 0.294657 0.000926128 0.000565056 0.000685412 0.294239 56 41 22 0.00129446 0.000643583 0.000860544 0.416518 0.00128053 0.000641873 0.000854761 0.410811 56 42 21 0.00095897 0.000527739 0.000671483 0.356436 0.000986408 0.00054246 0.000690451 0.355442 56 43 21 0.00126047 0.000576778 0.000804674 0.460586 0.00120436 0.000578402 0.000787051 0.4315 57 44 21 0.00141709 0.000815438 0.00101599 0.333322 0.00136115 0.000786714 0.000978188 0.330026 57 45 20 0.00107155 0.000547688 0.000722309 0.398732 0.0010439 0.000565023 0.000724638 0.366345 57 46 19 0.00106184 0.000688623 0.000813027 0.276355 0.00106565 0.000721324 0.000836098 0.250311 58 46 18 0.00138626 0.00111282 0.00120397 0.13344 0.00133896 0.00105932 0.00115254 0.147013 58 46 17 0.00190569 0.00154603 0.00166592 0.127639 0.0017048 0.00136742 0.0014799 0.141036 58 47 17 0.00182424 0.00136918 0.00152086 0.176476 0.00170912 0.00128364 0.00142549 0.178103 58 48 17 0.00179186 0.00155183 0.00163184 0.121897 0.0016827 0.00141198 0.00150224 0.137642 58 49 17 0.00173965 0.00152012 0.00159329 0.0828833 0.00156972 0.00134741 0.00142152 0.101404 58 50 17 0.00146827 0.00123617 0.00131354 0.105179 0.0013648 0.00113875 0.00121408 0.115824 59 51 17 0.000939683 0.000730799 0.000800427 0.151144 0.000913724 0.000729779 0.000791094 0.140851 59 52 17 0.000973182 0.000776841 0.000842288 0.136551 0.000937145 0.000762049 0.00082041 0.130533 59 53 17 0.000974158 0.000799803 0.000857921 0.120722 0.000938325 0.000778099 0.000831516 0.119775 59 54 17 0.00100004 0.000821513 0.000881023 0.135361 0.000956475 0.000793336 0.000847705 0.130042 # pathway end Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Freesurfer November 2016