Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Segmentation fault
by Ritobrato Datta 03 Aug '09

03 Aug '09

Hello All, I got this error when I ran recon-all -all. I changed machines and the same dataset went all the way through without any errors. I ran another dataset with the machine "taxi" and it ran fine. Any suggestions will be helpful. _________________________________________________________________________________________________________________ SUBJECTS_DIR is /jet/kadivar/freesurfer Segmentation fault Linux taxi.penn.edu 2.8.10-128.1.1.e5 #1 SMP Thu May 7 10:35:59 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Aug 1 06:20:17 EDT 2009 _________________________________________________________________________________________________________________ Thanks Ri Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology Center for Functional Neuroimaging University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. Philadelphia Pa 19104

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Postdoctoral Position, University of California, San Diego
by Don Hagler 02 Aug '09

02 Aug '09

Postdoctoral Research Scholar Position in Behavior Genetics and Neuroimaging Departments of Psychiatry and Radiology, University of California, San Diego The Departments of Psychiatry and Radiology at the University of California, San Diego are pleased to invite applications for a postdoctoral research scholar position in neuroimaging and behavior genetics under the direction of Drs. Anders Dale (Neuroscience and Radiology) and William Kremen (Psychiatry). Responsibilities will include analysis of MRI, genetic, and behavioral data collected for the NIH/NIA-funded Vietnam-Era Twin Study of Aging (VETSA). The successful candidate will receive training in psychometric techniques (particularly twin analyses) and the application and development of analysis tools for neuroimaging data (including structural MRI, DTI, fMRI, and ASL). The postdoctoral candidate will be encouraged to develop his or her own research projects that fit within the overall scope of the project. 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 structural MRI and DTI in VETSA wave 1. A variety of additional information was also collected, including neurocognitive, personality, and psychosocial assessments, medical history interviews, blood pressure, pulmonary function, and hormonal levels. DNA has been obtained from all subjects and they have been genotyped for APOE. Genome-wide genotyping of all VETSA subjects is planned. Wave 2 of the project will acquire five-year follow-up data, and also include fMRI and ASL scans. Applicants for the position must have completed relevant Ph.D. research activities within the past five years. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Experience or expertise in the following areas is highly desired: 1. computer programming (especially MATLAB, C/C++, or similar) 2. neuroimaging analysis methods (especially FreeSurfer) 3. structural MRI, DTI, fMRI, ASL 4. scientific writing 5. advanced statistical analyses 6. twin modeling (especially using Mx software) 7. genetics This posting 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 policies 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 your CV, a brief statement of research interests and goals, and any selected reprints to wkremen(a)ucsd.edu and amdale(a)ucsd.edu with the subject line "VETSA Postdoctoral position". Letters of reference will be required before final approval of hiring. Informal inquiries for more details are welcome. _________________________________________________________________ Get back to school stuff for them and cashback for you. http://www.bing.com/cashback?form=MSHYCB&publ=WLHMTAG&crea=TEXT_MSHYCB_Back…

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RES: Recon-all
by Pedro Paulo de Magalhaes Oliveira Jr 01 Aug '09

01 Aug '09

You can run n recon-all simultaneously where n is the number of cores you have in your machine. In a dual core 2 recon-all In a quad-core 4 recon-all In a MacPro with 8 core you can run 8 recon-all You also should have at least 1GB per recon-all Enviado do meu celular Nokia -----Msg original----- De: Jesse Bledsoe Enviada: 01/08/2009 18:52:57 Assunto: [Freesurfer] Recon-all Hi Everyone, How many reconstructions (recon-all) can one run at a time? It is working nicely (30 + hours) with one going but I have many subjects to reconstruct - can I run 4 or 5 without problems? Thanks, Jesse -- Jesse Bledsoe, M.A. Clinical Psychology Center for Neurodevelopmental Study Michigan State University 110E Psychology Building East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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Recon-all
by Jesse Bledsoe 01 Aug '09

01 Aug '09

Hi Everyone, How many reconstructions (recon-all) can one run at a time? It is working nicely (30 + hours) with one going but I have many subjects to reconstruct - can I run 4 or 5 without problems? Thanks, Jesse -- Jesse Bledsoe, M.A. Clinical Psychology Center for Neurodevelopmental Study Michigan State University 110E Psychology Building East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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freesurfer in Ubuntu 8.1 or 9.04
by Gonzalo Rojas 01 Aug '09

01 Aug '09

Hi: I want to install FSL under Ubuntu 8.10 or 9.04... There exist any problem, or I must use CentOS ?... Sincerely, Gonzalo Rojas Costa

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cerebral white matter volume
by saulg＠ualberta.ca 31 Jul '09

31 Jul '09

Hi there, In the aseg.stats file, there are two reports of cerebral white matter volume. The first report is near the top of the file, as such: # Title Segmentation Statistics # ... # surface-based-volume mm3 lh-cerebral-white-matter 172917.046875 # surface-based-volume mm3 rh-cerebral-white-matter 173269.906250 # surface-based-volume mm3 tot-cerebral-white-matter 346186.953125 ... The second report is lower in the file, contained in the section that would be turned into a spreadsheet by the 'asegstats2table' function: # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 2 167965 167965.0 Left-Cerebral-White-Matter 104.1714 8.0979 41.0000 131.0000 90.0000 ... 21 41 179570 179570.0 Right-Cerebral-White-Matter 102.5936 8.2544 50.0000 133.0000 83.0000 ... I noticed these numbers are consistently different, so I have two questions: 1) Why are they different? Is it because the first is surface based? 2) Which numbers should I use when reporting total cerebral white matter volume? Thanks so much!

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Freeview on Mac
by jentis＠nmr.mgh.harvard.edu 31 Jul '09

31 Jul '09

Hi Guys, Is it possible to get Freeview compiled for a Mac? Last time I check, it wasn't supported, but it would be of great help to me and at least a couple other members of my lab. Thanks. Best, Jon

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Flipped image talairach correction and missing .dcm extension
by Lena Palaniyappan 31 Jul '09

31 Jul '09

-- Hello group I am new to freesurfer. I have two problems. Please accept my apologies if these queries are bit naïve! Any help will be much appreciated. I am trying to autorecon1 a single image obtained from Philips 3T as dicom output. I use MacOS X11 terminal. 1. I am not able to use mri_convert to change these images to .mgz or niftii format. Is this because these files lack .dcm extension? For some reason all these files don¹t have .dcm extension though my radiology colleagues repeatedl assure me that they are dicoms! 2. I obtained some T1 MPRAGEs in img hdr format (no mat files came with them) and I am trying to recon1 this subject. There is a problem with talairach transforms (z 8) that needs manual correction. But when I try to open the brainmask.mgz on tkmedit for visual inspection I get the following msg Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Nevertheless when I proceed to open the tkregister2 for manual correction, ( without surf orig), I see the moveable image 180* flipped compared to the target image in sagittal view. Could this be due to some error in conversion of dcms? Or is this due to acquisition differences? Please help. Many thanks in advance Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [Freesurfer] Processing data with -noaseg flag
by Bruce Fischl 31 Jul '09

31 Jul '09

Hi Falk, can you really not afford the 6 minutes or so of scan time to get a good 1mm dataset? We have analyzed a bunch of 7T data successfully, although it probably isn't as automated as 1.5 and 3T. The error you are getting we only see when you have run out of disk space. It sounds like the surface file is corrupted. As for the cutting planes, you should be able to select a point in the pons above the cerebellar peduncle for the brainstem cutting plane. This should remove the cerebellum, which is required for analysis. We certainly did many cortical thickness studies before the aseg stuff was integrated into the stream, so it should be possible, it just requires more work. cheers, Bruce On Thu, 30 Jul 2009, Falk Lüsebrink wrote: > Hi FreeSurfers, > > > > As the subcortical segmentation fails fairly often on my high resolution > data I want to skip it by using the noaseg flag, but Im currently > encountering another issue. > > > > 1.) During the fix stage of autorecon2 I receive following error during > mris_euler_numbers (also if I want to view the lh.orig or rh.orig in > tksurfer): > > > > rh.orig: face[233615].v[2] = 119048, but face 233615 not in vertex 119048 > face list > > > > lh.orig: face[196300].v[1] = 100366, but face 196300 not in vertex 100366 > face list > > > > 2.) Normally the subcortical segmentation is also used to cut both > hemisphere and to remove the cerebellum. The cutting plane between the > hemispheres is done very well, but I have never been able to remove the > cerebellum. Do I need to remove it manually or are there some ways to remove > it automatically? Is it required to be removed? > > > > 3.) Im interested in measuring cortical thickness only. But do I need to > keep something else in mind while not using the subcortical segmentation to > process my data? > > > > > > Thanks in advance, > > Regards, > > Falk > >

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mghRead error
by leemon albert 31 Jul '09

31 Jul '09

Hi, I am running Ubuntu 8.04 and freesurfer V4.3.0. It worked well once upon a time. However, I get this error about the mghRead as follows. *~$ recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/** liwentao_1.mgz* Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux /usr/local/freesurfer/subjects/liwentao_1 mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... Linux nica 2.6.24-24-generic #1 SMP Tue Jul 7 19:46:39 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Fri Jul 31 09:20:08 CST 2009 I try to run it step by step: *~$ mri_convert /mnt/data2/data/trauma/**liwentao_1.mgz /usr/local/freesurfer/**subjects/liwentao_1/mri/orig/**001.mgz* mri_convert /mnt/data2/data/trauma/liwentao_1.mgz /usr/local/freesurfer/subjects/liwentao_1/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $ reading from /mnt/data2/data/trauma/liwentao_1.mgz... mghRead: encountered error executing: 'zcat /mnt/data2/data/trauma/liwentao_1.mgz',frame -1,errno=38 There is sufficient disk space for freesurfer running. I searched the mail-archive and noticed the potential solutions. But it doesn't work. Any suggestion is appreciated! -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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