Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

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unable to download freesurfer
by Davis, Peter 27 Jan '14

27 Jan '14

Hi, I am unable to download free surfer. Is there a problem at the ftp? Thank you, Peter

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Diffusion analysis artifact
by Rotem Saar 27 Jan '14

27 Jan '14

Dear freesurfer experts, I'm using the attached script to perform diffusion analysis for 3T Philips dicoms, 16 gradients. I want to end with a specific FA value for each segment. During the analysis I noticed an artifact (see attached pic) which I don't really understand. I double-checked my data using DICOM-viewer and some other DTI software and the data seems fine - no artifacts (I but I don't want to use other software, as I already performed volumetric analysis to these subjects using freesurfer and now interested to expand the volumetric results and give both volume+FA values to each segment). Another question I have is regarding the FA values I get - for example, I'm getting CC fa values between 0.45-0.75 - does this make sense ? Shouldn't they be more like 0.6-0.8 ? (subjects are healthy students, age range: 25-30). Can u please look at the script and highlight what I'm doing wrong ? Will you agree to look at my data if I will send a folder with one subject ? Thanks in advance Rotem 1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy1627/DTI/I160.dcm --s Anatomy1627 --o /usr/local/freesurfer/subjects/Anatomy1627/DTI --b /usr/local/freesurfer/subjects/Anatomy1627/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy1627/DTI/bvecs.bvec To check results, run: tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy1627/DTI/lowb.nii --reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/register.dat --surf 2) tkmedit Anatomy1627 orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/register.dat -overlay /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa.nii -fthresh 0.2 -fmax 1 3) mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa.nii --targ /usr/local/freesurfer/subjects/Anatomy1627/mri/orig.mgz --s Anatomy1627 --interp nearest --o /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii --reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/register.dat To check results, run: tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii --targ /usr/local/freesurfer/subjects/Anatomy1627/mri/orig.mgz --reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii.reg 4) mri_mask /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii /usr/local/freesurfer/subjects/Anatomy1627/mri/brainmask.mgz /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.mask.nii To check results, run: tkmedit Anatomy1627 /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.mask.nii 5) mri_segstats --seg /usr/local/freesurfer/subjects/Anatomy1627/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.mask.nii --sum /usr/local/freesurfer/subjects/Anatomy1627/stats/all_stats_fa_Anatomy1627 Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev Beer-Sheva 84105 Israel

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Postdoctoral Research Position in Neuroimaging of Eating Disorders
by Geisler, Daniel 27 Jan '14

27 Jan '14

The Eating Disorder Section of the Department of Child and Adolescent Psychiatry, University Hospital Carl Gustav Carus, Dresden University of Technology, Germany (Prof. Stefan Ehrlich) invites applications for a postdoc position (full time) in neuroimaging of eating disorders with a focus on computational neuroscience and in close collaboration with the Collaborative Research Centre 940 "Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions" http://www.sfb940.de/. Our international and multidisciplinary group conducts basic research in neuroscience at the inter-face to clinical applications. We focus on cognitive control, reward system and the processing of positive and negative emotions in patients with anorexia nervosa. Some of our projects are part of the aforementioned Collaborative Research Centre (CRC, Steering Committee: Profs. T. Goschke, C. Kirschbaum, M. Smolka, A. Strobel, H.-U. Wittchen). Postdoctoral Research Position (f/m) in Neuroimaging of Eating Disorders To further strengthen our lab, we are seeking for a postdoc with some experience in Computational Neuroscience, e.g. model-based analysis of behavioral and MRI data, decoding or machine learning. Responsibilities will also include the coordination of our ongoing clinical research study and the acquisition, preprocessing and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Together with a doctoral student new functional MRI paradigms need to be programmed and implemented. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner. We routinely collect high-quality structural, diffusion, and functional MRI data. A variety of additional information is also being collected, including neuropsychological and psychiatric scales, physiological (SCR, eye tracking) and endocrinological markers. Summarizing results and writing research articles will be another central aspect of the work. The successful applicant will work in a team of young investigators and also start to supervise doctoral students, interns and medical students working in the project. Thanks to the CRC the applicant will have ample opportunity to work with peers and senior scientists in similar project in the Medical School and the Psychology Department. In addition, the position offers the possibility for further scientific qualification (i.e. Habilitation). Requirements: * Doctoral degree (Ph.D.) in any scientific field of study with a strong quantitative background, e.g. mathematics, informatics, statistics, computational neuroscience, biomedical or electrical engineering (with additional qualifications or experience in computational neuroscience a PhD, MD or comparable degree in a relevant field such as psychology, biology, biomedicine, medicine, biophysics or physics may also be sufficient). * Expertise in computational modeling of behavioral and/or imaging data (e.g., Bayesian inference methods and statistics, hidden Markov modeling, machine learning, reinforcement and temporal difference learning or connectivity analyses) * Experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB) * Some exposure to cognitive and emotional neurosciences * Participation in research activities within the past years * Publications in peer-reviewed journals * Strong organizational skills * Command of some basic German The successful applicant will join a multidisciplinary team of researchers and clinicians, will receive further training and train doctoral students (informally). The Salary will be consistent with levels in accordance with the German Research Foundation (100% TV-L: E 13). Compensation includes health insurance and vacation time. The position is available for a start date as soon as January 20th 2014 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for two to three years with the possibility of renewal after positive evaluation. The funding has been granted for 5 years. To apply you can use our online portal (http://www.uniklinikum-dresden.de/bildung-und-karriere/stellenangebote/wiss… ). The application should include a cover letter detailing professional objectives and interests, CV (with grades and language skills), and the names and email addresses of two references. The application can be written in German or English. The position is open to qualified international applicants. Please refer to our homepage: http://www.kjp-dresden.de/en/content/eating-disorders , http://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_na…, http://www.kjp-dresden.de/en/content/schizophrenia and http://www.kjp-dresden.de/de/basic-page/publikationsliste-prof-dr-s-ehrlich for more detailed information. ::::::::::::::::::::::::::::::::::::::::: Dipl.-Inf. Daniel Geisler Wissenschaftlicher Mitarbeiter Bereich Angewandte Entwicklungsneurowissenschaften Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Fon +49 (0)351 458-7071 Fax +49 (0)351 458-7206 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74 (Haus 25, Raum 232), 01307 Dresden http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 201 145 00020

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-qcache / fsaverage / number of vertices errors
by Mihaela Stefan 24 Jan '14

24 Jan '14

Hello FreeSurfers, I am trying to run a group analysis with Qdec following this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freev… I got a series of errors when I ran: recon-all -s <subjid> -qcache .... ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ... mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ... Reading source surface reg /home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/lh.sphere.reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014 One of the errors says "number of vertices in... does not match surface." I found an older post where someone else was complaining about the same error and Doug suggested running "recon-all -surfvolume ..." https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-September/025737… I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors. Can someone help me sort this out? Thank you, Mihaela

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Advice: Freesurfer Parallel Processing on Large Dataset
by Elijah Mak 24 Jan '14

24 Jan '14

Hi FSL Experts, I am currently processing a large dataset and would like to seek some advice regarding parallel processing. These are the specifications of my iMac: 3.2GHz , Intel Core i5, No. of processor: 1, Total number of cores: 4, L2 Cache per core: 256kb, L3 Cache: 6MB, Memory: 8GB. Would it be useful to open 4 terminals and run RECON-ALL on 4 subjects simultaneously? Lastly, is there some sort of -flag I can use to maximize parallel RECON-ALLs ? Currently, I am running 2 RECON-ALLs on 2 terminals and each subject take on average 7-9 hours for completion, which is rather fast I think. Many Thanks. Best Wishes, Elijah -- Elijah Mak, B.A. Doctoral Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ

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(no subject)
by Hugh Pemberton 24 Jan '14

24 Jan '14

Hi freesurfer crew, I found some details through this website http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/i… about cortical thickness maps with freesurfer. I have done some reading but can't really make much sense of how I might do this for a single subject through freesurfer. I have already done autorecon 2 and 3 and so have the cortical thickness stats but would like to put it into a map such as this one: [image: [Click to enlarge image]]<http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/f…> Could you possibly advise on how I might go about this? Would be much appreciated. Many thanks and all the best, Hugh

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Source Code not accessible
by Thomas Frank 24 Jan '14

24 Jan '14

Hello, I tried to get freesurfer's source code after registering and receiving the password for the read-only-cvs. The login command from https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS is simply failing with a timeout like this: # cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login Logging in to :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:2401/usr/fscvsroot CVS password: cvs [login aborted]: connect to fsvm.nmr.mgh.harvard.edu(155.52.242.23):2401 failed: Connection timed out The timeout happens even when I do not use the correct password. Does anyone has any suggestions? Best regards, Thomas

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Editing-related Wiki pages
by Harms, Michael 24 Jan '14

24 Jan '14

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converting binary cortical GM ribbon mask to mative T1 space
by Alexopoulos, Dimitrios 24 Jan '14

24 Jan '14

Hi, We'd like to map the cortical GM ribbon on our original single volume native space anatomical T1. The dataset has been run through recon-all -all. The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the cortical GM mask in freesurfer space, correct? I converted the ribbon.mgz to native T1 space using: mri_label2vol --seg ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz Is this the correct procedure? Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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converting binary cortical GM ribbon mask to native T1 space
by Alexopoulos, Dimitrios 24 Jan '14

24 Jan '14

We'd like to map the cortical GM ribbon on our original single volume native space anatomical T1. The dataset has been run through recon-all -all. The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the cortical GM mask in freesurfer space, correct? I converted the ribbon.mgz to native T1 space using: mri_label2vol --seg ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz Is this the correct procedure? Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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Freesurfer January 2014