Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

failure on 1 of the allen institute brains
by Satrajit Ghosh 05 Jul '13

05 Jul '13

hi bruce and others: i'm getting a recon failure on this particular brain: H0351.1009 the quality isn't great, but if you can take a quick look at the brain to see if you can spot any particular issues, that would be great. 4 of the others finished recon and 3 are almost there. cheers, satra data location: http://human.brain-map.org/mri_viewers/data command: recon-all -subjid H0351.1009 -all -i /data/allen/H0351.1009/T1.nii.gz -openmp 8 -notalairach ==> /data/subjects/H0351.1009/scripts/recon-all-status.log <== status file for recon-all Fri Jul 5 00:02:39 UTC 2013 #@# MotionCor Fri Jul 5 00:02:43 UTC 2013 #@# Nu Intensity Correction Fri Jul 5 00:02:57 UTC 2013 #@# Intensity Normalization Fri Jul 5 00:04:45 UTC 2013 #@# Skull Stripping Fri Jul 5 00:07:53 UTC 2013 Linux node007 3.2.0-39-virtual #62-Ubuntu SMP Thu Feb 28 00:48:27 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s H0351.1009 exited with ERRORS at Fri Jul 5 00:16:26 UTC 2013

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tkmedit and freeview show different control points
by Sebastian Urchs 05 Jul '13

05 Jul '13

Hi, I am trying to migrate to freeview from tkmedit and started comparing edits in both programs. I found that when I set control points in tkmedit and then load tmp/control.dat in freeview as a point set, the control points in freeview do not match those in tkmedit. In fact, the ones in freeview seem to be scattered randomly. Could this be casued by wrong settings or is there a known fix for this? I attached a screenshot to explain the problem better. Thanks, Sebastian

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Re: [Freesurfer] retinotopic mapping selxavg3-sess error
by Bianca van Kemenade 05 Jul '13

05 Jul '13

Hi, I just wanted to let you know that I solved the problem by creating a new virtual machine on which I installed the newest version of Ubuntu (13.04), FSL, and Freesurfer manually. I guess there could have been a solution with the virtual machine running Xubuntu via the Freesurfer virtual disk image, but I didn't manage to figure it out so I decided to take this longer route. Anyway it seems to run well now! Best, Bianca On Mon, Jun 24, 2013 at 11:36 AM, Bianca van Kemenade < biancavankemenade(a)gmail.com> wrote: > Sorry for the delay. I'm new to FSL, Freesurfer, and VB, so maybe I'm > doing it wrong, but I have the impression I cannot run FSL from the VB: > - Typing 'fsl' yields 'fsl: Command not found'. > - Checking the environment with 'echo $FSLDIR' yields 'FSLDIR: undefined > variable' > - Checking the path with 'flirt -version' yields 'flirt: Command not found' > > However, typing 'fsl' + tab shows the following available commands: > - fsl2par > - fsl_label2voxel > - fslmaths.fsl > - fslorient.fsl > - fslregister > - fslregister -sess > - fsl_rigid_register > - fslsfonts > - fsl_sub_seychelles > - fslswapdim.fsl > > So it seems there are some FSL-related files installed, but apparently not > all. I did download the virtual disk image for Freesurfer, so I assumed a > complete FSL version would be included? I'm sorry if there's an obvious > solution, but I can't seem to find it... > > Thanks again, > Bianca > > > On Fri, Jun 21, 2013 at 6:16 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> >> Can you run FSL at all in your VB? >> >> >> >> >> On 6/21/13 7:49 AM, Bianca van Kemenade wrote: >> >> Dear Freesurfers, >> >> I'm setting up freesurfer to do retinotopic mapping. I use a PC with >> Windows XP, so I installed Freesurfer using the VirtualBox (with Xubuntu). >> I managed to get through the initial steps for retinotopic mapping, but I >> get stuck at the actual analysis. >> >> The point where I get stuck is: >> >> selxavg3-sess -a rtopy.self.lh -s P2_BK >> >> It starts the analysis, but runs into problems at the stage "Using >> FSL's BET to extract brain" and gives the following error output: >> >> # ---------- Using FSL's BET to Extract Brain------------------ # >> /home/virtualuser/freesurfer/ >> shared/P2_BK/bold >> bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1 >> /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found >> /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found >> /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found >> [: 158: =: unexpected operator >> /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found >> /bin/rm: cannot remove `_tmp*': Protocol error >> ERROR: bet failed >> >> I tried updating FSL in case that is the problem, but it is only >> available for Ubuntu 10.04 and up, whereas the Ubuntu system that is >> provided to install the Freesurfer virtual disk image is 9.04. If anyone >> has an idea how to proceed let me know, any help is much appreciated. >> >> Thanks, >> Bianca >> >> >> >> _______________________________________________ >> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> 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. >> >> > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > > > > -- > Bianca van Kemenade, MSc > Doctoral Candidate, Berlin School of Mind and Brain > > Klinik für Psychiatrie und Psychotherapie > Campus Charité Mitte > Charitéplatz 1 > 10117 Berlin > http://www.mind-and-brain.de/ > -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/

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Software Engineering positions in NGS, Novartis, Cambridge, MA
by Bailey, Pam 04 Jul '13

04 Jul '13

The Novartis Institutes for BioMedical Research is the global pharmaceutical research organization for Novartis. For our new Next Generation Diagnostics (NGDx) group being launched at our global headquarters in Cambridge, MA, we are seeking two Software Engineers. Sr. Software Engineer, Sequencing - http://novartis.avature.net/ngdx/jobDetail?id=222 Design, build & support a high-throughput, fault-tolerant pipeline management solution for the interpretation of large and complex data sets in a distributed, cluster-compute environment. Integrate new tools and reporting techniques into pipeline as needed. Software Engineer - http://novartis.avature.net/ngdx/jobDetail?id=221 Design and implement LIMS/workflow execution support from sample accession thru NGS analysis, work with lab users to define LIMS functionality & workflow requirements, participate in the technical development process for genomics platforms , including next-generation sequencing platforms, and work with automation team and lab users to implement lab automation. Both positions require skills in one or more of the following programming languages: Java, Python, C#, Perl, C#, C++, Ruby, as well as demonstrated experience with database programming and interfaces, preferably in MySQL or Oracle. Previous experience with SVN, GIT or similar version control systems is essential. Please click on the urls above for a more information about the NGS group, and more complete descriptions of the jobs or to apply.

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Software Engineering positions in NGS, Novartis, Cambridge, MA {Disarmed}
by Bailey, Pam 04 Jul '13

04 Jul '13

The Novartis Institutes for BioMedical Research is the global pharmaceutical research organization for Novartis. For our new Next Generation Diagnostics (NGDx) group being launched at our global headquarters in Cambridge, MA, we are seeking two Software Engineers. Sr. Software Engineer, Sequencing - http://goo.gl/seY8S Design, build & support a high-throughput, fault-tolerant pipeline management solution for the interpretation of large and complex data sets in a distributed, cluster-compute environment. Integrate new tools and reporting techniques into pipeline as needed. Software Engineer - http://goo.gl/YUDuT Design and implement LIMS/workflow execution support from sample accession thru NGS analysis, work with lab users to define LIMS functionality & workflow requirements, participate in the technical development process for genomics platforms , including next-generation sequencing platforms, and work with automation team and lab users to implement lab automation. Both positions require skills in one or more of the following programming languages: Java, Python, C#, Perl, C#, C++, Ruby, as well as demonstrated experience with database programming and interfaces, preferably in MySQL or Oracle. Previous experience with SVN, GIT or similar version control systems is essential. Please click on the urls above for a more information about the NGS group, and more complete descriptions of the jobs or to apply.

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NU_evaluate crash while running Longitudinal Analysis with FS 5.3
by Salil Soman 04 Jul '13

04 Jul '13

Hi, I have been trying to run the FS longitudinal analysis on a subject with 3 time points. I ran each time point thourgh FS, made the template, but when I run the last step I do not get mri/norm files and the output files state nu_evaluate: crashed while running mincmath (termination status = 768), see attached log. Any suggestions on what I am doing incorrectly? Best wishes, Sal Salil Soman, MD, MS

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Contrast matrix for per-vertex regressor
by Elisa Scariati 04 Jul '13

04 Jul '13

Dear freesurfers, I'm currently making a per-vertex analysis using the --pvr flag of mri_glmfit. I already made within-group correlations between thickness and lGI correcting for age and gender that worked perfectly. However, when I tried to make a between groups comparison, I ran into an error and I'm wondering if I did it correctly. I want to compare the slope of the pvr between my groups, so I will use a DODS design. In my fsgd file I have the following columns: group, age, gender. So, counting my pvr, I should have in my contrast matrix 2*(3+1)=8 columns. I made my contrast this way : 0 0 0 0 0 0 1 -1 However, when running mri_glmfit, I get the following error: ERROR: dimension mismatch between X and contrast C22qVScon.txt X has 7 cols, C has 8 cols As my matrix file has 6 columns corresponding to what would be expected from my fsgd file (two for group, gender and age, that contain the correct values), it seems that there is only one column added for the pvr instead of two. Do anyone know if I made a mistake or is it not possible to compare pvr between groups this way? Thank you in advance for your answer, Best regards Elisa

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How to maximize the number of subjects on a machine?
by ye tian 04 Jul '13

04 Jul '13

Dear Freesurfers, I am currently running 4 subjects, each on a separate x11 window. With 19 subjects at hand and subsequent manual editing, I can't resist the temptation to open more x11 terminals and to submit more jobs. However, how do I know that I max out the machine's computing power? Hard drive info Processor Name: Intel Core i5 Processor Speed: 2.7GHz Number of Processors: 1 Total number of cores: 4 Memory: 16GB Thank you very much! Sincerely, Ye

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cerebellum
by clelia pellicano 04 Jul '13

04 Jul '13

Dear all, it is just a simple question. How reliable are the cerebellum WM and cortex volumes? There is any kind of manual editing for this structure? Thank you so much, Clelia

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Available post doc position
by Anders Martin Fjell 03 Jul '13

03 Jul '13

Available post doc/ PhD position At the Research group for lifespan changes in brain and cognition (LCBC) at the University of Oslo (Norway), we have an available post doc position on the project "Patterns and mechanisms of brain atrophy in healthy aging and dementia: Why is the aging brain susceptible to Alzheimer's Disease?" We will also consider applications from excellent PhD candidates. Deadline for applications is August 15th, and expected start date will be October 2013. The position is for three years. The position The successful candidate will work on the multi-center international project "Patterns and mechanisms of brain atrophy in healthy aging and dementia: Why is the aging brain susceptible to Alzheimer's Disease?" financed by the Norwegian Research Council. MRI, PiB PET/ CSF Abeta and cognitive data from large samples of elderly participants, MCI patients and AD patients will be analyzed. The candidate will be heavily involved in these analyses, as well as in writing papers on the results. The yearly salary for a post doc candidate will be equivalent of approximately 82.000-92.000 USD, while the yearly salary for a PhD candidate will be equivalent of approximately 71.000-80.000 USD. Requirements In addition to a formal background with a master or PhD in a relevant field, such as informatics/ physics/ mathematics, psychology, medicine, neurobiology/ neuroscience, the candidate needs excellent skills in neuroimaging. Expertise in FreeSurfer and preferably FSL will be important. Some programming skills, e.g. MatLab, Python etc, are also necessary. The candidate needs to be excellent in English, both oral and in writing. Interest and expertise in Alzheimer Disease research will also be an advantage. The research group The project is coordinated from Research Group for Lifespan Changes in Brain and Cognition (LCBC) at the Department of Psychology, University of Oslo, Norway. LCBC is a very active research group, and currently includes 16 full-time positions (faculty, post docs, PhD candidates). The project involves extensive collaborations with several AD centers and neuroimaging centers in the US and Europe. Bruce Fischl and Doug Greve from Harvard (FreeSurfer) and Steve Smith and Heidi Johansen-Berg from Oxford (FSL) are collaborators on the project and will participate in the neuroimaging analyses. The candidate will take active part in this collaboration. Link to the application form can be found here: http://uio.easycruit.com/vacancy/1001919/65775?iso=gb If you have questions or want more information, please contact PI Anders M Fjell (andersmf(a)psykologi.uio.no) -- Anders M Fjell Professor of cognitive psychology Research Group for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo www.oslobrains.no

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Freesurfer July 2013