Freesurfer

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30088 discussions

Re: [Freesurfer] thalamic nuclei additional scan error
by Iglesias Gonzalez, Eugenio 23 Nov '18

23 Nov '18

External Email - Use Caution Dear Zhac, Apologies for the mistake in the wiki. As explained in the error message, the subjects directory is the second argument. Also, if you are using a T2 scan, I would replace t1 by t2 in the last argument. The call should be: (For a T1 additional scan) segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/ /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1 (For a T2 additional scan) segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/ /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t2 Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of zhac looch <Z30D(a)hotmail.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 23 November 2018 at 16:32 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] thalamic nuclei additional scan error External Email - Use Caution Hi Freesurfer Team, I want to add additional scan my thalamic segmentation. but my code is not working. where is the error in my code? thanks for help my code: segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1 my error: Usage: segmentThalamicNuclei.sh SUBJECT_ID [SUBJECT_DIR] [ADDITIONAL_VOL ANALYSIS_ID BBREGISTER_MODE] Or, for help segmentThalamicNuclei.sh --help

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thalamic nuclei additional scan error
by zhac looch 23 Nov '18

23 Nov '18

External Email - Use Caution Hi Freesurfer Team, I want to add additional scan my thalamic segmentation. but my code is not working. where is the error in my code? thanks for help my code: segmentThalamicNuclei.sh MS14 /Applications/freesurfer/subjects/MS14/mri/orig/T2raw.mgz T2 t1 my error: Usage: segmentThalamicNuclei.sh SUBJECT_ID [SUBJECT_DIR] [ADDITIONAL_VOL ANALYSIS_ID BBREGISTER_MODE] Or, for help segmentThalamicNuclei.sh --help

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White brainmask.mgz
by Rosalia Dacosta Aguayo 23 Nov '18

23 Nov '18

External Email - Use Caution Dear Free Surfer experts, I am experiencing a problem with 4 participants. Whrn I open the brainmask with freeview, it appears white (binarized). I was editing this brainmask and at sone point I switched something and it changed to white. I deleted alk the files and I run recon-all - autorecon1. The problems persists and recob-all -autorecon1 finished with errors. I do not know how to solve this problem. I would much appreciate your help. Best regards, Rosalia

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Fsgd-File
by Larissa Bechtle 23 Nov '18

23 Nov '18

External Email - Use Caution Hi freesurfer-experts, I am currently trying to run mris_prepoc. However FreeSurfer keeps telling me that there are no subjects specified. Thus, I think that the fsgd-file I created is the problem. I already checked it several times but still don’t know what’s wrong. I would be very thankful for some tips. -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni [kpsy-mac84024:~/Desktop/larissa/Gewalt] Forschung% setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt/ [kpsy-mac84024:~/Desktop/larissa/Gewalt] Forschung% mris_preproc --fsgd FSGD.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gewalt.10.mgh ERROR: no subjects specified [kpsy-mac84024:~/Desktop/larissa/Gewalt] Forschung% GroupDescriptorFile 1 Title Aggression Class Group1 Class Group2 Variables Age Input zv75 Group1 27 Input xp09 Group1 26 Input wn79 Group2 24 Input wi40 Group1 19 Input vg03 Group1 33 Input va82 Group2 24 Input ui42 Group2 23 Input ud16 Group1 26 Input tp38 Group2 22 Input to98 Group2 22 Input th01 Group1 23 Input tg08 Group2 23 Input so80 Group2 21 Input re37 Group1 27 Input pt12 Group2 27 Input pl96 Group2 22 Input pi04 Group2 27 Input oo75 Group1 22 Input ob56 Group2 23 Input nh85 Group2 27 Input mw53 Group2 23 Input lu75 Group1 22 Input lt62 Group2 22 Input le00 Group1 23 Input lc79 Group2 24 Input kp89 Group1 22 Input ko71 Group2 25 Input ke93 Group1 29 Input ju55 Group1 20 Input jc49 Group1 21 Input in19 Group2 29 Input if27 Group1 29 Input hc55 Group2 23 Input gs02 Group1 43 Input fp50 Group2 21 Input ez57 Group2 25 Input et53 Group2 24 Input ei77 Group2 27 Input dn20 Group2 28 Input cp97 Group1 25 Input cn18 Group2 52 Input cm66 Group1 21 Input cg21 Group2 22 Input bw90 Group1 29 Input bg38 Group2 25 Input ab35 Group1 22 Best, Larissa

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Problem with freesurfer installation on mint 19 (ubuntu based OS)
by Mahshid Fouladivanda 23 Nov '18

23 Nov '18

External Email - Use Caution Hi Dear experts, I downloaded and installed freesurfer on CentOS without any problem and also worked with it. Recently I've switched on mint 19 (an Debian based operating system) and I tried to setup freesurfer but, it does not worked. I would appreciate your help to make it work on ubuntu (or mint). Regards, Mahshid

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Re: [Freesurfer] Problem with freesurfer installation on mint 19 (ubuntu based OS)
by fsbuild 23 Nov '18

23 Nov '18

External Email - Use Caution Hello Rashid, I would start with getting a cmake command to succeed to try and do the build.  Try looking over the cmake build page here,  https://surfer.nmr.mgh.harvard.edu/fswiki/CMake - where there is also makefile (makefile.wiki) you can download that should default to some useful settings for the cmake command on CentOS 6, 7, Ubuntu 16, 18, and MacOS   If you are on debian it will probably default to the CentOS 7 settings, but you could start from there. - R. Mahshid Fouladivanda November 23, 2018 at 06:49         External Email - Use Caution         Hi Dear experts,   I downloaded and installed freesurfer on CentOS without any problem and also worked with it. Recently I've switched on mint 19 (an Debian based operating system) and I tried to setup freesurfer but, it does not worked. I would appreciate your help to make it work on ubuntu (or mint).   Regards, Mahshid   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview showing results in a strange manner
by 姜时泽 22 Nov '18

22 Nov '18

External Email - Use Caution | | Dear freesurfer experts, I am using freesurfer to analyze my PET data according to the tutorial online. It works pretty well and I write the values of the results of each region to the template with Matlab (file attached here entitled "lh.subj1.mgz"). However, when I try to open it with freeview, the image looks quite strange ('Picture_1') but it works with tksurfer (Picture_2). Does any one know what is wrong with this? Did I plot the result in a wrong way? Thanks very much Shize -- Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13(a)fudan.edu.cn | | | |

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Freeview fly through frames
by Hervé Lemaitre 22 Nov '18

22 Nov '18

External Email - Use Caution Dear Freesurfer users, I want to use the "Save Movie Frames..." in freeview to go through 305 frames of an overlay on a pial surface. When a select: Fly through Frame Start number 0 End number 305 Step size 1 I click "write" and it writes only one image and stops. Thanks for you help. Freeview 2.0 Ubuntu 16.04 Hervé LEMAITRE Faculté de Médecine Université Paris-Sud 63, rue Gabriel Péri 94276 Le Kremlin-Bicêtre

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Average subject normal data base
by m s 22 Nov '18

22 Nov '18

External Email - Use Caution Hi, I am looking forward to create a normal database for daily use to compare with individual patient mr volumes. I was thinking about creating an average subject from a normal database of multiple subjects. After I have my average subject, would it be posssible and correct to compare this average recon individually to a new subjects recon, redoing all the averaging and comparing process only between this two? Thank you Mercedes

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Deadline approaching: Deadline approaching: Neuroscience data analyst (f/m) opening at ENI Göttingen, Germany (new opening)
by Caspar M. Schwiedrzik 22 Nov '18

22 Nov '18

External Email - Use Caution The European Neuroscience Institute Göttingen (Germany) is seeking a *Neuroscience data analyst (f/m) * initially limited until 31.12.2019 with extension options, full-time | salary according to TV-L The European Neuroscience Institute is looking to fill the position of a data analyst (full time). We are looking for a data analyst with interest and experience in systems neuroscience. Research at the European Neuroscience Institute ranges from molecular biology to human psychophysics and involves a range of model organisms (from drosophila to non-human primates), techniques and approaches (electrophysiology, two-photon imaging, fMRI, EEG, behavior). The data analyst will work closely with all of the various research groups at the European Neuroscience Institute, supporting research efforts, e.g., through modelling and statistical analyses of high-dimensional data, image processing, and programming/development of experiments. S/he will have the opportunity to develop and publish, e.g., analytical tools that arise from this work. - The applicant should possess a university degree (minimally M. Sc. or equivalent) in a relevant field, e.g., statistics, biostatistics, informatics, or similar. Prior experience in the field of systems neuroscience is highly desired. - The applicant should have experience in a research setting utilizing quantitative methods and statistics. The applicant shall demonstrate strong analytical skills and knowledge of novel and emerging analysis techniques is highly desired. Future/forward thinking in the area of big data analytics/informatics and applying them to contribute to the research groups’ scientific process is expected. - The applicant should be skilled in the analysis of multivariate datasets to reveal patterns and build models; conduct exploratory data analysis, and communicate with team lead/team members; identify improvements for existing data management and recommend requirements for new systems. - Contribute to replicability by making suggestions for existing data management and recommend requirements for new systems and identify potential data integrity issues. We are committed to open data/open science and appreciate interest and expertise in this area. - Utilize programming languages such as Python, Matlab and/or C++. - Good command of English is mandatory. The University Medical Center Göttingen takes flexible account of the individual design of working hours at the workplace. It is interested in implementing the wishes of its employees as far as possible. If you are interested in this job and have specific questions about working hours, please contact us. Women are especially encouraged to apply. Applicants with disabilities and equal qualifications will be given preferential treatment. We look forward to receiving your application by * November 30th, 2018* University Medical Center Göttingen European Neuroscience Institute Göttingen Dr. Caspar Schwiedrzik Group Leader Grisebachstr. 5 37077 Göttingen Tel.: 0551/39-61371 Fax: 0551/39-61399 E-Mail: c.schwiedrzik(a)eni-g.de <+c.schwiedrzik(a)eni-g.de> Web: http://www.eni-g.de/ Please send your application only via e-mail as a PDF-file. also see: http://www.med.uni-goettingen.de/de/content/service/stellenanzeigen.php?id=…

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