Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

a problem
by yczhang 20 May '08

20 May '08

Using lgi or thickness,how could I know the anatomical correspondence for a statistical difference area which had been found between patients and controls. Thanks! yczhang 2008-05-21

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Question regarding computing contrasts with mri_glmfit
by Avram Holmes 20 May '08

20 May '08

All, I'm just looking for a little advice on constructing fsgd and .mat files. I would like to compare a healthy control sample with the data from two MDD groups. To do so I made my fsgd file to look like the following: GroupDescriptorFile 1 Title MoneyGame_Subjects Class Control Class MDD Class Anhedonic Input REWARD111 Control Input REWARD201 Anhedonic Input REWARD207 MDD Input REWARD208 Anhedonic Input REWARD211 MDD Input REWARD212 MDD Input REWARD213 Anhedonic Input REWARD215 Anhedonic Input REWARD277 Control Input REWARD278 Control .... This file results in a design matrix with 3 columns. I am interested in conducting the following analyses and I wanted to check to see if I am coding all of the .mat files correctly. Controls vs all Patients (1 -.5 -.5) Anhedonic vs MDD (0 1 -1) Controls vs Anhedonic (1 0 -1) Controls vs MDD (1 -1 0) Thank you in advance for any help you can offer. Avram -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Possible to regress whole-brain functional data against continuous variables in the volume?
by Dan Dillon 20 May '08

20 May '08

Hi FreeSurfers. Is it possible to regress functional data against a continuous variable in the volume? I'm analyzing a reward processing study that activates sub-cortical and cortical regions, and I'd like to regress those data against a continuous measure of depressive symptoms administered to each participant. I understand the basic fsgd/mri_glmfit approach from the FS tutorial, but I want to stay in the volume in order to examine sub-cortical structures (e.g., nucleus accumbens). Is this possible? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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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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Freesurfer