Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30133 discussions

Monte Carlo Simulation Precomputed Data
by Natasha Haris 27 Jan '14

27 Jan '14

Dear Freesurfers, I am slightly confused about the monte carlo simulation. First off, I only find a blob when I run the p<0.05 threshold level and don't see anything else when I run simulations with p less than that. What does this mean? Additionally, when I click on any question of interest after running this p<0.05 simulation (for ex. "Does the average thickness, accounting for Group, differ between male and female?" I get the same blobs that I found before I ran this precomputed simulation. Is the simulation not running correctly? Am I supposed to enter this threshold value (1.3) into the area marked Threshold min= and max=5. Thank you for your help! Natasha

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unable to download free surfer
by Davis, Peter 27 Jan '14

27 Jan '14

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

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mri_glmfit-sim for volume data: GRF vs. simulation
by Susan Ruiz 27 Jan '14

27 Jan '14

Hi FreeSurfers, I was just reading this post to the archive (below) regarding using mri_glmfit-sim on volume data, and it suggests that using --grf rather than doing the simulation can be "inaccurate at low smoothness and low thresholds." At what smoothness values and threshold values should we opt to use the simulation over GRF for volume-based cluster corrections? Thanks, ~Sue Ruiz > Hi Yuko, it should be performing Gaussian Random Field (GRF) > cluster-wise correction. Based on the smoothness, the size of the search > space, and the voxel-wise threshold, it attempts to compute the p-value > of resulting clusters. The differences between GRF and doing the > simulation are that GRF runs almost instantly but it can be inaccurate > at low smoothnesses and low thresholds. It looks like the GRF was not > implemented until 5.1 doug yukoyy wrote: >* Dear all, *>>* I'm conducting volume based group analysis and corrections for multiple comparisons. *>* My environment :Mac OS 10.6.8, Freesurfer 5.0.0 *>>* I followed the instruction I found here: *>* http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel> *>>* When I first successfully ran: *>* mri_glmfit --y ces.005.nii --wls cesvar.005.nii --osgm --glmdir F2glm.wls --nii.gz *>* tkmedit fsaverage orig.mgz -aparc+aseg -overlay F2glm.wls/osgm/sig.nii.gz -fminmax 3 7 *>>* Then, I wanted to do corrections for multiple comparison. *>* mri_glmfit-sim --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 *>>* However, FreeSurfer does not seem to recognize --grf, and I don't understand what does grf do. *>* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% *>* ERROR: Flag --grf unrecognized. *>* --glmdir F2glm.wls --grf 3.0 pos --cwpvalthresh .0166 *>* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% *>>* I chose to use --grf because it was suggested in the tutorial, and in FreeSurfer mailing list archive. *>* http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20573.html <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20573.html> *>>* I am guessing that I cannot use --cache for volume analysis because I don't have *>* /Applications/freesurfer/average/mult-comp-cor/fsaverage/volume/cortex/fwhm12/pos/th30/mc-z.csd *>>* I also tried monte-carlo simulation, and it worked okay. *>>* So, here is my question. *>* What does --grf do? and Is there any documentation? *>>* Thank you! *>* Yuko Yotsumoto *>* yukoyy at a7.keio.jp <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* _______________________________________________ *>* Freesurfer mailing list *>* Freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>>> -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 -- * * ** *** ***** ******** ************* Susan Mosher Ruiz, Ph.D. Research Scientist Boston University School of Medicine Laboratory of Neuropsychology VA Boston Healthcare System smosher(a)bu.edu * * ** *** ***** ******** *************

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Inquiry about Choi's striatum parcellations.
by 조수연 27 Jan '14

27 Jan '14

p{margin:0;padding:0;} Hello, I'm a FreeSurfer beginner and would like to ask a question about Choi's stratium parcellations. I was doing a research to incoorporate the parcellations by Choi on my subjects' images to delve further to understand the distincitve characteristics of each parcels. I decided to use the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz. Since my images were on the standardized model from FSL, I transformed Choi's image to the MNI standard using FIRST of FSL. Since both images were now on the same MNI space, I viewed both of them on FSL to make sure that the Loose mask covered my image completely, but found that the tail bit of my image was a couple of pixels too longer than Choi's Loosened mask. Do you think there is a way that I can further "loosen" up Choi's image to fit my image? Or can you recommend me a different solution to this problem? I'll wait for your reply. Thanks! Sincerely, Sooyun Cho.

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Post-Doc position available at Aix-Marseille University
by Olivier Coulon 27 Jan '14

27 Jan '14

Dear all, a post-doc position is available at Aix-Marseille University, France, on the topic of "descriptors of cortical folding patterns in the developing brain". Please see document attached. If you are interested, please contact Dr Julien Lefèvre (julien.lefevre(a)univ-amu.fr) -- Olivier Coulon, CNRS research Fellow, olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univmed.fr> Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr <http://olivier.coulon.perso.esil.univmed.fr/> LSIS Laboratory, I&M Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE BrainMorph logo http://www.lsis.org/brainmorph

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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

1 0

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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