Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

Research Associate position in Nottingham (UK)
by Dave Langers 04 Feb '13

04 Feb '13

Research Associate MRC Institute of Hearing Research Nottingham, United Kingdom Salary £26,022 – £28,178 per annum http://www.topcareer.jobs/Vacancy/irc81869_2735.aspx The aim of this post is to contribute to the understanding of the pathogenesis of tinnitus in humans by analysing a large set of existing anatomical MRI scans. This is an ideal position for an early career scientist to work in a research Institute with worldwide reputation and develop their knowledge and expertise. The project aims to produce research output of high quality to further the MRC’s scientific mission and to contribute to the field of tinnitus research within the UK. You will work with Dr Peyman Adjamian and Dr Dave Langers from the National Hearing Biomedical Research Unit and be part of the Neurophysiology and Histology group led by Professor Alan Palmer, where research is aimed at investigating the structure and function of the auditory system. One area of research interest in this group is the mechanisms underlying the perception of tinnitus using brain imaging techniques Magnetoencephalography (MEG) and functional MRI in humans. The position does not require collection of MRI data, but experience with existing MRI analysis software is highly desirable. Results will be disseminated in national and international conferences and findings published in peer-reviewed journals. You will be expected to deliver the project described above in the period specified as well as contribute to scientific discussions in related fields of auditory science. You will be expected to support the smooth functioning and productivity of the research team. For more information regarding this role please email Dr Peyman Adjamian Peyman.Adjamian(a)ihr.mrc.ac.uk. Applications are handled by the RCUK Shared Services Centre; to apply please visit our job board at http://www.topcareer.jobs/. If you are unable to apply online please contact us on 01793 867003 quoting reference IRC81869. Closing date: 24 February 2013 Interview date: 27 March 2013 The MRC is an Equal Opportunities Employer Final appointments will be subject to a pre employment screening This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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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R: Re: tracula bvecs error
by stdp82＠virgilio.it 03 Feb '13

03 Feb '13

Hi Anastasia, I have put T1 in /Applications/freesurfer/subjects/subject_prova/Diff01/ together data.nii.gz, bvals and bvecs.My $SUBJECTS_DIR=$FREESURFER_HOME/subjects/subject_provaT1 was called as T1_01.nii.gz. This is well done? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 3-feb-2013 20.50 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] tracula bvecs error Do you have a freesurfer recon of your subject's T1 in the $SUBJECTS_DIR? On Sun, 3 Feb 2013, stdp82(a)virgilio.it wrote: > I think that I have resolved the bvecs error by using sudo nano option but > now in the next step I visualize this error: > ERROR: fio_pushd: > /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mni > ERROR: must specify brain mask volume for output subject > > Thanks, > > Stefano > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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tracula bvecs error
by stdp82＠virgilio.it 03 Feb '13

03 Feb '13

I think that I have resolved the bvecs error by using sudo nano option but now in the next step I visualize this error: ERROR: fio_pushd: /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/mniERROR: must specify brain mask volume for output subject Thanks, Stefano

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tracula bvecs error
by stdp82＠virgilio.it 03 Feb '13

03 Feb '13

Hi Anastasia, Any news? I checked my environment and it's ok. LANG="en_US.UTF-8"LC_COLLATE="en_US.UTF-8"LC_CTYPE="en_US.UTF-8"LC_MESSAGES="en_US.UTF-8"LC_MONETARY="en_US.UTF-8"LC_NUMERIC="en_US.UTF-8"LC_TIME="en_US.UTF-8" I have previously used the files that I send to you to perform FSL analysis without problems. What can I do to resolve my problem about bvecs? Thank you very much. Stefano ----Messaggio originale---- Da: no-reply(a)nmr.mgh.harvard.edu Data: 1-feb-2013 12.03 A: <stdp82(a)virgilio.it> Ogg: FileDrop Upload Information Hey! You recently uploaded the following files to the Martinos Center FileDrop: -> data.nii.gz (273.67 MiB) -> T1_01.nii.gz (10.91 MiB) -> bvals.txt (0.08 KiB) -> bvecs.txt (0.31 KiB) Here are the people you sent these files to: -+ ayendiki(a)nmr.mgh.harvard.edu In case you'd like to modify some of the above information, please use the link below: http://gate.nmr.mgh.harvard.edu/filedrop2/?g=wc4i0ky Hope you have a great day! ~ The NMR Team The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Is the server down?
by Francis Manno 03 Feb '13

03 Feb '13

I was wondering if the sever was down? Im trying to download freesurfer its not working. Ive tried all the different downloads and still no response: http://surfer.nmr.mgh.harvard.edu/fswiki/Download I was trying to get the windows version: * ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Virtu… * -- Ciao Francis Manno

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cvs freesurfer cvs [checkout aborted]: cannot expand modules
by Knut J Bjuland 03 Feb '13

03 Feb '13

Hi could you please add information about how to download from cvs? cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P -r dev Give this error message cvs [checkout aborted]: must specify at least one module or directory Knut J

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bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19
by Knut J Bjuland 03 Feb '13

03 Feb '13

When I run recon-all using freesurfer 5.2 latest beta it will segment crash. Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/knutjbj/freesurfer/ernie mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz Segmentation fault Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013 For more details, see the log file /home/knutjbj/freesurfer/ernie/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Knut J

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Inaccurate transformation
by Shani Ben Amitay 03 Feb '13

03 Feb '13

Dear freesurfers I used bbregister to coregister diffusion images with anatomical. I would like to apply the bbregistration transformation to the white and pial surfaces What I've done is: I calculated new transformation matrix using fs_read_dat.m and then apply it to the surfaces with mri_surf2surf. When overlaying the new surface on the diffusion data- it seems that the transformation is inaccurate.(screenshot is attached) Any idea why?. Thanks, Shani

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FS 5.2-beta run-times on Amazon Web services (AWS)
by Mehul Sampat 02 Feb '13

02 Feb '13

Hi Folks, Just wanted to share our experience with running FS 5.2-beta on Amazon Web Services (AWS). Basically, AWS has multiple instance types ( http://aws.amazon.com/ec2/instance-types/) and we were trying to figure out the most cost-effective approach. We ran two subjects through FS 5.2-beta on M1 Large Instance (m1.large) and Cluster Compute Eight Extra Large Instance (cc2.8xlarge). (same subjects run on both instance). We expected cc2.8xlarge to be faster (but it is also more expensive: $2.4 per hour; 8 cores); The run-times we got: instance-type subject start-time end-time run-time m1.large subject-1 01:05:44 UTC 2013 15:40:45 UTC 2013 *~14hr-35mins* m1.large subject-2 01:06:06 UTC 2013 15:08:45 UTC 2013 *~14hr-02mins * cc2.8xlarge subject-1 01:26:38 UTC 2013 12:30:23 UTC 2013 *~11hr-04mins* cc2.8xlarge subject-2 01:27:28 UTC 2013 12:19:08 UTC 2013 *~10hr-52mins* Although m1.large is a few hours slower, it seems to be the more cost effective option since it is $0.24 per hour (2 cores). If you have run Freesurfer on AWS, do you have a similar experience ? Any suggestions to speed up the run-times on AWS would be very helpful. Thanks Mehul

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Freesurfer parcellations: raw MRI or after resetting the origin?
by Sudhin A. Shah 02 Feb '13

02 Feb '13

Hello, I have been running Freesurfer parcellations on my raw MRI. Is it better to first reset the origin (Step 5 herehttp://www.mccauslandcenter.sc.edu/CRNL/sw/tutorial/html/eventspm.html) BEFORE parcellating? Thanks, S

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Freesurfer February 2013