Freesurfer May 2008

freesurfer@nmr.mgh.harvard.edu

63 participants
95 discussions

cannot allocate memory problem when using make average subject
by Jiefeng Jiang 20 May '08

20 May '08

Hi, I was trying to build an average subject using 250 subjects and I got the following error message: processing subject nor76 (246 of 250) reading spherical surface /DATA_FREESURFER/Data/nor76/surf/rh.sphere.reg... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) curvature mean = -0.017, std = 0.597 curvature mean = -0.064, std = 0.640 ripping medial wall... computing parameterization for surface /DATA_FREESURFER/Data/nor76/surf/rh.inflated.H... ImageAlloc: could not allocate 512x256 buffer curvature mean = -0.088, std = 0.872 Cannot allocate memory I saw someone discussing this issue a few month ago and Doug provided new scripts of make_average_subject, make_average_volume and make_average_surface to solve this problem. However, I can't find these files using the link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Can anyone tell me whether and how this problem has been solved? Thanks in advance! Jiefeng Jiang

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Porting Freesurfer data
by Navaneethan Santhanam 19 May '08

19 May '08

Hi Freesurfer gurus & experts, I'm trying to port Freesurfer data into an Afni-compatible format. I have some questions regarding this process - 1. I came up with the idea of converting Freesurfer data to the Analyze format (from the PDF on the FSWiki), and then to Afni. I'm not exactly sure how to create Analyze's .img files, as there doesn't seem to be any documentation on this. Is there a way to do this, or am I heading down an overly complicated route? Is there a better way to convert Freesurfer data into Afni's format? 2. Given .mgz files, I tried gunzip-ing them, but received an error saying that the extension was an unknown format. How do I unzip these files? I'd really appreciate any help you can give me. Thanks, Navaneethan -- Navaneethan Santhanam Department of Computer Science University of Illinois at Urbana-Champaign Contact - 1-217-714-6954

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ipfsl failed
by jake＠nmr.mgh.harvard.edu 19 May '08

19 May '08

Hello, I received the following error: (csh executable, ran from /autofs/homes/014/jake/AnalysisPrograms/CD_DMRFASL_ctrl2_ContrastAnalysis.csh) /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2 Mon May 19 10:16:02 EDT 2008 /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold /space/amaebi/35/users/ablood/DMRF_ASL RunList 019 020 021 022 023 024 ---------------------------------------------- /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold ipfsl -i 019/fmc4 -o 019/fmcsm4 -pct .1 -fwhm 4 -fmt bhdr ---------------------------------------------- ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed bugr: REESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects (looking at logfile, for the command dir is /space/amaebi/35/users/ablood/DMRF_ASL.) PWD: /space/amaebi/35/users/ablood/DMRF_ASL/log (logfile in log directory is preproc-CD_DMRFASL_ctrl2-bold.log) If anyone can help me, (im new to this) I would greatly appreciate it. Thank you in advance, Jake

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error on reconall2 stage
by xinian zuo 18 May '08

18 May '08

Hi, FSers I performed auto-reconall script and faced an error in below command, mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance bao-xin Segmentation fault Anyone can give me suggestions how to look for further details about it? I do this under altix3700 system and use freesurfer 4.0.3 (i.e., freesurfer-Linux-suse-ia64-stable-pub-v4.0.3-full.tar.gz). Thank you! Best Xi-Nian -- WEB: http://zuoxinian.googlepages.com/home BLOG: http://zuoxinian.blogspot.com/ MOTTO: Research is no ending cycle! Many cycles in the brain! Mathematics is a kind art!

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Tksurfer dimples
by Ming Hsu 16 May '08

16 May '08

Hi, I have a couple of newbie questions on using freesurfer. I was able to reconstruct the data without too much trouble, and now am at the quality check stage. We spotted a couple of small "dimples" on the tksurfer surface (attached). Upon inspecting the uninflated views in tkmedit, however, it's not clear what is causing it. We don't see any obvious misclassification of gray or white matter, understandable I suppose given it's quite a small imperfection. How do people usually try to find the underlying problem in these cases? Also how much of an imperfection is considered "significant". Also another issue that I found quite strange. When we find the coordinate in tksurfer, and try to input it into tkmedit, the program would show a coordinate that is somewhere near (but not all that close, between 10-20mm) to the actual inputted coordinate. Not sure why that would be, but it makes going between tksurfer and tkmedit more cumbersome. BTW, thanks for the great software and the wiki. Ming Hsu

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Freesurfer vs. VBM
by Martin Kavec 15 May '08

15 May '08

Gentlemen, I am giving a lecture about aging brain. I only discuss freesurfer, since that's the method we use for the brain volume and cortical thickness assessment. There are other methods, such as VBM and SIENA potentially providing similar information. I would appreciate if you could point me to a reference, which compares features of Freesurfer and VBM, or if you could provide me your insight on what are the advantages of FreeSurfer over VBM. I could think of the following: 1. Freesurfer allowes for the subvoxel precision of the volume estimation 2. VBM involves strong filtering in order to suppress variations of individual anatomies 3. ???? 4. ???? 5. ???? Thanks a lot in advance. Martin

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Ph D scholarships at School of Psychiatry , University of New South Wales, Sydney, Australia
by wanlin 15 May '08

15 May '08

- *Ph.D Scholarships in Neuroimaging * *School of Psychiatry, University of New South Wales, Sydney, Australia* The School of Psychiatry at UNSW invites applications for a Ph.D. Scholarships in the area of brain Magnetic Resonance Imaging (MRI), to commence in the 2^nd half of 2008. Each scholarship is for $27,500 p.a. for a maximum of 3 years, The Scholarships will focus on the broad areas of current interest: computational analysis of multidimensional and longitudinal MRI data and MRI correlates of cognitive disorders in late life. This scholarship is offered as part of the _Brain and Ageing Program, UNSW <http://psych.med.unsw.edu.au/psychweb.nsf/page/brainage>_, a high profile research program funded by the _NH&MRC <http://www.nhmrc.gov.au/>_, which aims to evaluate the determinants of age related cognitive disorders. The successful doctoral students will be working with data derived from two study cohorts of international significance (the Memory and Ageing Study and the Older Australian Twins Study). The successful applicants will work in close collaboration with our international research partners, Applicants are encouraged from students/researchers from a variety of backgrounds including but not limited to engineering, mathematics and computer science, with mathematical/statistical and computer programming aptitude and strong interests in neuroimaging. For further details, please contact Dr. Wei Wen (by phone +61-2-93823730, email: _W.Wen(a)unsw.edu.au <mailto:W.Wen@unsw.edu.au>_ ) or Dr. Julian Trollor (by phone +61-2-93823763, email: _J.Trollor(a)unsw.edu.au <mailto:J.Trollor@unsw.edu.au>_) or Prof. Perminder Sachdev (+61-2-93823763, _P.Sachdev(a)unsw.edu.au <mailto:P.Sachdev@unsw.edu.au>_ )

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Hippocampal volumes
by p.s.bjerkan＠studmed.uio.no 15 May '08

15 May '08

Hi, We have been using your exellent software for some time now. We work on several studies and in one of them we now asess the hippocampus volume. The information is gathered from the Freesurfer aseg.stats file. The data for this group has been run in both versions 3.0 and 4.0. When comparing results from these runs we find discrepant results. We have four questions: 1) I assume that some degree of difference in outcome between the two FS versions is to be expected. But how large a difference would you consider "normal" or acceptable? Our differences seem to be quite large. I have attached the outputs for lh. for two subjects with extensions fs3 (Freesurfer 3.0) and fs4 (Freesurfer 4.0). 2) I have inspected the subjects with the largest discrepancies and so far it seems that it is v4.0 that is producing the errors. The tiffs attached showing where I believe there are obvious errors (the fs4´s). 3) Is it possible to edit aseg results? (or is that only for the cortical reconstructions?) 4) Can you give any advise on which of the data sets we should do calculations on? Have also attached a Excel-file with the volumes for all the subjects in the study (average and STD on the bottom...). If this large variations is to be expected, small changes in subject groups (about 3-5 per cent) could be missed. Thank you ! Petr

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color schematic
by Elif SIKOGLU 15 May '08

15 May '08

Hello, We have created a difference map (surface encoded volume). We would like to display different values on the map as different colors (similar to an annotation file). Is there a way to convert a surface encoded volume to an annotation format or even label files? Thanks, Elif

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Freesurfer vs. VBM in SPM
by Juergen Haenggi 15 May '08

15 May '08

Hi FS and VBM experts I also tried to compare FS and VBM in SPM a time ago. We decided not to compare cortical thickness (FS) with absolute volume (VBM). We multiplied the FS thickness by the FS area vertex-wise to construct FS volume maps (the not yet implemented step) and compared them with absolute volume (modulated, VBM). Suppose I had done everything right, the resulting FS volume maps were subjected to analysis and showed nearly identical results as that derived from only the thickness map analysis. It seems that there is almost no variability in the FS area maps, right? Should we use FS thickness maps or FS volume maps when comparing FS with classical VBM (SPM, FSL)? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Freesurfer May 2008