Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

3D visualization of subcortical volumes
by Alexa Nardelli 11 Apr '09

11 Apr '09

Hi, I have used FreeSurfer volumetrics to obtain various volumes of some subcortical structures. I would like to obtain a 3D image of each of these subcortical structures. I have tried importing the volumes into Matlab, however Matlab doesn't recognize the mgz file. Any suggestions on how I could go about doing this? Thanks, Alexa

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Re: [Freesurfer] Two problems.
by gmszh 10 Apr '09

10 Apr '09

Hi Bruce, Thanks for the reply. So I will do recon-all -talairach for all subjects using version 4.30 and obtain the new eTIV, keeping the segmentation and surface data unchanged. Is that the correct way? And can someone please help me with problem #1? Thanks, Zheng Hui On 8/4/09 20:51, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Zheng, > > I'll leave 2 for Nick. As for 1, we don't use the tal very much, and a > bad tal will not affect your thickness estimates. The newer versions > rarely have a bad tal since we changed over to Avi Synder's code (which > also fixes the problems we had with eTIV). You can manually correct it > using tkregister2, although this is probably only needed if you want to > report tal coords (or average in tal space). > > cheers, > Bruce > > On Wed, 8 Apr 2009, gmszh wrote: > >> Hi all, >> >> I have two problems here. >> >> 1. talairach.xfm >> By browsing through the mailing list, it seems that talairach.xfm was >> not used much in the recon-all process which is quite different from the >> table given at >> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps. We did find >> many subjects with bad talairach transformation but reasonable segmentation >> and surface reconstruction (version 3.05). Are the results (volumes and >> cortical thickness) for those subjects still trustworthy? Can you kindly >> clarify the importance of talairach.xfm in the pipeline? And since the new >> method of eTIV uses this transformation, is there any way to ensure manual >> registration is fine enough to be used for this estimation, if I have to >> manually register those subjects mentioned above? >> >> 2. recon-all -long >> We processed our data with the longitudinal pipeline. So far we only >> found 6 subjects failed among 200 subjects (tp1 corrected). All these 6 >> subjects seemed to have problem during the registration from tp2 to tp1. I >> used the command "tkmedit -f tp2.long.tp1/mri/orig.mgz -aux >> tp2.long.tp1/mri/orig_tp1_to_tp2.long.tp1.mgz" and realized they were not >> aligned. I have tried different cost functions using >> "fsl_rigid_registration". All of them gave the same result. Is there any way >> I can do the manual registration? I used "fsl_rigid_registration" because no >> matter which cost function I specified to recon-all -long, it would call >> "fsl_rigid_registration" with corratio as the cost function. >> >> Thanks in advance, >> Zheng Hui >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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Talairach Failure
by Andrew Jahn 10 Apr '09

10 Apr '09

Hi, I got the following error when trying to run recon-all on an MP-RAGE T1-weighted image: Fri Apr 10 16:25:01 EDT 2009 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Fri Apr 10 16:25:02 EDT 2009 /usr/local/freesurfer/subjects/MPRAGE/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Darwin The-Ohio-State-University-Server.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 And this was the command I typed: recon-all -subject MPRAGE -i fmprage.nii -all auto-recon works for other T1's using a FLASH sequence, for example, but failed on this one. Any help would be greatly appreciated. Thank you! -Andrew

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removing background
by slew＠nmr.mgh.harvard.edu 10 Apr '09

10 Apr '09

Hi, I want to remove the background 0 in the segmented volume like aseg.mgz, and saved the volume without the background. What is the simplest way to do it? Best, Seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail slew(a)nmr.mgh.harvard.edu FAX 617 726 7422

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Postdoctoral Research Scholar Position in Behavior Genetics and Neuroimaging
by Christine Fennema Notestine 10 Apr '09

10 Apr '09

Postdoctoral Research Scholar Position in Behavior Genetics and Neuroimaging Department of Psychiatry, University of California, San Diego The Department of Psychiatry at the University of California, San Diego is pleased to invite applications for a postdoctoral research scholar position in behavior genetics and neuroimaging under the direction of Drs. William Kremen (Psychiatry) and Anders Dale (Radiology and Neuroscience). The position focuses on training in the application of sophisticated psychometric techniques (particularly twin analyses) and neuroimaging methods (structural MRI , DTI, fMRI, and ASL) that will be applied to the NIH/NIA-funded Vietnam Era Twin Study of Aging (VETSA) in collaboration with investigators at Boston University, Massachusetts General Hospital, and Virginia Commonwealth University. VETSA is a unique longitudinal study of over 600 middle-aged male twin pairs that focuses on understanding cognitive and brain aging. Over 500 twins have undergone 3D structural MRI and DTI in VETSA wave 1. These twins also underwent extensive neurocognitive assessment, personality and psychosocial measures, a medical history interview, in-lab physical health measures such as blood pressure and pulmonary function, and hormonal assays for cortisol, testosterone, and DHEAS. DNA has been obtained from all subjects and, to date, they have been genotyped for APOE. Genome-wide genotyping of all VETSA subjects is planned. Wave 2 of the project, which was recently funded, will acquire five-year follow-up data, and also include fMRI and ASL scans. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Requirements for the position are: 1) completion of relevant Ph.D. research activities within the past five years; 2) advanced writing and advanced statistical or neuroimaging skills, and 3) an interest in imaging genetics research. Experience with multilevel data analysis, twin modeling, genetics, and/or neuroimaging is desirable. The postdoctoral candidate will be encouraged to develop his or her own research projects that fit within the overall scope of the project. The position will entail immersion in twin modeling (e.g., using Mx software) and MR image analysis including FreeSurfer and other methods. This advertisement is for a 2-year appointment beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego for Postdoctoral trainees. Compensation includes full staff benefits, including health insurance, and vacation time. Review of applications will begin immediately and will continue until the position is filled. To apply, please send a copy of your CV, a brief statement of research interests and goals, and any selected reprints to the address below. Letters of reference will be required before final approval of hiring. Informal inquiries concerning this position are encouraged. Please e-mail wkremen(a)ucsd.edu for more details. William S. Kremen, Ph.D. Department of Psychiatry University of California, San Diego 9500 Gilman Drive (MC 0738) La Jolla, CA 92093-0738 -- Christine Fennema Notestine, Ph.D. Asst Professor of Psychiatry and Radiology University of California, San Diego Phone: 858-822-3198 / 858-246-0605 E-mail: fennema(a)ucsd.edu Fax: 858-534-1078

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Dense annotations
by Alex Fornito 09 Apr '09

09 Apr '09

Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file. Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes. Does this limit have something to do with what is specified in the colortable.orig_tab structure? We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else? Thanks for your help, Alex -- Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email: af397(a)cam.ac.uk Phone: +44 (0) 1223 764670 Fax: +44 (0) 1223 336581 Australian Details: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 1 & 2, Alan Gilbert Building 161 Barry St Carlton South 3053 Victoria, Australia Email: fornitoa(a)unimelb.edu.au Phone: +61 3 8344 1861 Fax: +61 3 9348 0469

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mri_glmfit
by Lusineh Gharapetian 08 Apr '09

08 Apr '09

Hello, I'm trying to use the mri_glmfit function but keep running into the same error. I am using the FSGD format and have set up my fsgd file according to the tutorial instructions: " GroupDescriptorFile 1 Title mci_age_BNTchange Class Male Class Female Variables Age BNTchange Input Subject1 Male 70 2 Input Subject2 Female 75 -3 Input Subject3 Female 72 0 etc." Our .mat file states: " 0 0 0 1" indicating that "BNTchange" is our variable of interest. We are attempting to run a DOSS analysis. The line of code I type into the terminal is: " mri_glmfit --glmdir mci_age_bntchange_lh --y dv-visit2-lh.mgz --fgd mci_age_bntchange.fsgd doss --C mci_age_bntchange.mat" This results in the following error: "ERROR: matrix is illconditioned or badly scaled, condno = 1e+08" We have tried runninf this off of different versions of Freesurfer (R302 and R305) and cannot figure out how to fix this error. Any help would be appreciated! Thanks! - Lusineh Gharapetian

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Md5sum download mismatch
by john.dornisch＠scra.org 08 Apr '09

08 Apr '09

Hello, I am having a problem downloading the latest version of freesurfer 4.3. On 2 separate servers on 2 separate days I get the same md5sum which does not match the md5sums listed in the md5sum file in the downloads section. your md5s 29450bd531d94909cc858384551d43b0 freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0-full.tar.gz df4c679702d3bf01c458276a93a90547 freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz My md5sums 54de93353546c88ed9dc7b9de0b2384d freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz 6da2363ffc42e9c65a22033ad057748c freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0-full.tar.gz Please advise. Thanks John Dornisch

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mri_ca_train parameters?
by Jamie Hanson 08 Apr '09

08 Apr '09

Hi Freesufer folks- I was just about to start constructing a custom aseg atlas and I wondered if there were any recommendations for any of the optional flags? Any parameters yield better results (especially for specific brain regions)? I was focused on improving amygdala segmentation for my structural images (hence my asking). Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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RES: [Freesurfer] libvtkpng.so.5.2 missing?
by Pedro Paulo de Magalhaes Oliveira Junior 08 Apr '09

08 Apr '09

run yum list | grep vtk | grep png Sent from my Nokia phone @E71 -----Msg original----- De: Derin Cobia Enviada: 08/04/2009 15:56:27 Assunto: [Freesurfer] libvtkpng.so.5.2 missing? We're running subjects under the new 4.3.0 version (CentOS 4 platform), and are experiencing the following error during the cortical ribbon mask stage: -------------------------------------------------------------------------------------------- #@# Cortical ribbon mask Wed Apr 8 07:12:20 CDT 2009 /disk/NIACAL/human/freesurfer/conte_mprage_v4.3/020319_2263/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 -- label_right_white 41 --label_right_ribbon 42 --save_ribbon -- save_distance 020319_2263 mris_volmask.bin: error while loading shared libraries: libvtkpng.so. 5.2: cannot open shared object file: No such file or directory Linux heinz 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Apr 8 07:12:21 CDT 2009 -------------------------------------------------------------------------------------------- It appears that libvtkpng.so.5.2 does indeed not exist (in fact, no libvtkpng* files were found) in ~/freesurfer/lib/vtk/lib/vtk-5.2 for the current 4.3.0 CentOS 4 (32-bit) distribution we have, but found them present in our 4.1.0 (32-bit) and 4.3.0 (64-bit) distros . This may just be a case of "the missing libraries," but are they supposed to be gone? If not, are we safe to just copy them into the 4.3.0 vtk dir as a short term fix? Thanks. -Derin _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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