Freesurfer

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30135 discussions

Freesurfer 6 exits with errors after recon edits on skullstrip
by Tuominen, Lauri Johannes 10 Dec '15

10 Dec '15

Dear Freesurfer experts, I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but part of the occipital cortex was missing and I therefore ran the following command ( both in freesurfer6 ): recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib This took care of the brain mask problem that I had with the previous recon. So I then ran on launchpad: recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1' The last command exits with errors. Please find the log-files attached. Thank you for your help! Best, Lauri Tuominen

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ABCD postdoctoral position at Florida International University
by Anthony Dick 10 Dec '15

10 Dec '15

Dear Colleagues, Please find below an advertisement for our Postdoctoral position at Florida International University, Miami, FL. Details are also provided in the attached pdf. Thank you! Anthony >>> The Cognitive Neuroscience and Imaging Center at Florida International University (FIU) in Miami is seeking a full-time, benefits-earning Visiting Postdoctoral Fellow with expertise in magnetic resonance imaging (MRI) physics, with emphasis on functional MRI and diffusion- weighted MRI. The successful candidate will join a team of investigators to develop, support, facilitate, and coordinate daily data collection activities for the Adolescent Brain Cognitive Development (ABCD) Study: a landmark multi-site NIH study to assess the short- and long-term impact of substance use on brain development (http://addictionresearch.nih.gov) The successful candidate will develop, deploy, and optimize multiband fMRI and high angular resolution diffusion imaging (HARDI) acquisition protocols for use at 3T. She/he will contribute to deploying these MRI techniques, as well as prospective motion correction (PROMO), and fast, integrated distortion correction methods. These methods will be collectively applied in a large, longitudinal study designed to advance addiction science through a strong focus on developmentally informed assessment. The primary duties/responsibilities of the position involve direct engagement in magnetic resonance imaging (MRI) data collection efforts, including (but not limited to): protocol development and management, execution of research plan, implementation of experiments, data acquisition, and data management. Applicants must have a PhD in physics, biomedical engineering, radiological sciences, computer science, or a related field. Candidates must have a strong background in MR physics, as well as strong skills in computer programming (e.g., python, MATLAB). Applicants must have experience in MR scanner operation and software, image reconstruction, advanced data analysis (e.g., FSL, AFNI). Experience in multiband fMRI and/or HARDI imaging technology, and familiarity with data harmonization across multi-center imaging studies are highly desired. The applicant should ideally possess outstanding writing and communication skills as demonstrated by a successful publication record. The starting date for this position is January 1, 2016, and the salary will be commensurate with experience. To apply, please include all documents in one PDF file: cover letter, CV, a one-page statement describing your qualifications and research interests, contact information for two references, and copies of up to two of your publications. Applications should be sent via email to: cnic(a)fiu.edu. Review of applications will begin immediately. For informal enquiries regarding this position, please contact Dr. Angela Laird (alaird(a)fiu.edu) Additional information about the Center can be found at http://cnic.fiu.edu, and more information about the ABCD Project can be found at http://www.drugabuse.gov/news- events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain- development. MRI Postdoc -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: faculty.fiu.edu/~adick

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mri_label2vol --fill-ribbon argument
by Arnaud Boré 10 Dec '15

10 Dec '15

Dear Freesurfer's expert, I want to create a 3d volume using an annot file and I'm using mri_label2vol command. When running this command line: mri_label2vol --annot sub1/label/lh.Yeo2011_7Networks_N1000.annot --identity --subject sub1 --hemi lh --o sub1/mri/lh.Yeo.nii.gz --temp sub1/mri/T1.mgz --proj frac 0 5 0.1 I get a 3d volume but the ribbon is not well filled so I wanted to use --fill-ribbon available with Freesurfer 6 but then I get a binary volume 3d of the ribbon without any information I had from my annot file. Is there an error with this --fill-ribbon option ? How can I get this 3d volume of the ribbon from annot file ? Thank you Arnaud

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Errors when testing freesurfer installation
by Peng Zan 10 Dec '15

10 Dec '15

Dear freesurfer experts, I am new to freesurfer and I met this problem when I was testing freesurfer installation following the instructions on the 'Testing Freesurfer' website. I got the problems as follows when I tested command, 'tkmedit bert orig.mgz' on heavy data from tutorial web. Couldn't create output file .xdebug_tkmedit-------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. I have had the 'license.txt' file under FREESURFER_HOME folder, and the freeview works fine. I also created a 'fs.license' file under the home folder and copied the license info into it, but it still did not work. May you give any suggestions to fix this problem? Thank you! Looking forward to your reply! Sincerely, Peng

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summary files and figures from Monte Carlo simulation
by Karl Liu 10 Dec '15

10 Dec '15

Dear Experts, After running Monte Carlo simulation from the command line, I noticed two cluster summary files are produced for each contrast: cache.th20.neg.sig.cluster.summary and mc-z.neg.th20.sig.cluster.summary. They are quite similar, with different number of surviving clusters in some cases. I am wondering which is the one to report final results. Will you explain a bit more about the differences between them? Also, after reading the summary file, we still have to visualize the results. If the MC simulation is done in QDEC GUI, then the QDEC automatically presents the outcome from mc-z.neg.th20.sig.cluster.mgh, but I am not sure if this is the right file. I am using FS version 5.3 without tksurferfv. I found the tksurfer is running quite slow and unresponsive. Any other suggestions? Thank you very much!

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FreeSurfer 6 recon-all exiting with errors at -cortparc step
by Zaretskaya, Natalia 10 Dec '15

10 Dec '15

Dear all, I am running recon-all with FreeSurfer 6 stable version on launchpad and have it exiting with errors with all of my 43 brains, always at the same stage (-cortparc). The same brains used to run through recon-all smoothly with the dev version just a month or so ago, and I am not doing anything essentially different than before, except using FreeSurfer 6, so I am wondering what’s wrong. The output of recon-all before the error looks o.k. I attached an example recon-all.log file. Many thanks in advance for your help! Natalia

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Qdec question
by sabin khadka 10 Dec '15

10 Dec '15

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks

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Brainstem Substructures in Freesurfer 6.0 - how to calculate left/right volumes
by Chris Steward 10 Dec '15

10 Dec '15

Hello, I've installed Freesurfer 6.0 beta, and run the -brainstem-structures option to recon-all. The results look ok, but I'd like the left/right volumes for the superior cerebellar peduncle (SCP), rather than the total volume. Is there any easy way to do this? Thanks, Chris

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May you help me with 'recon-all' errors
by Peng Zan 09 Dec '15

09 Dec '15

Dear freesurfer expert, I am a student from University of Maryland, learning freesurfer for MNE analysis recently. I have a perhaps silly problem and could not solve by myself. The problem occurred as 'recon-all -s R2261_S0283 exited with errors...' when I was running 'recon-all -autorecon-all -subjid R2261_S0283'. I tried several subjects and got the same error. I am wondering whether you can look at the 'recon-all.log' file and 'recon-all.error' file and help me figure out what the problem is and how to solve it? Thank you very much! Looking forward to your reply! Sincerely, Peng

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Processing macaque data
by Mahmoud 09 Dec '15

09 Dec '15

Dear Experts, I am trying to modify the HCP pipeline scripts to work with macaque data (in vivo, 0.5mm isotropic). The Pipeline uses FSL and a FreeSurfer. In FreeSurferPipeline.sh there are some steps I'm not sure how to modify them to work correctly with macaque data instead of the human data: 1- recon-all -i "$T1wImageFile"_1mm.nii.gz -subjid $SubjectID -sd $SubjectDIR -motioncor -talairach -nuintensitycor -normalization >From what I've learned so far the option -talairach works with MNI305 template. Do I need to provide a macaque equivalent template instead of the MINI305? if yes, what would be the best way to convert my macaque template to MNI305? 2- mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz "$SubjectDIR"/"$SubjectID"/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta "$SubjectDIR"/"$SubjectID"/mri/T1.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz The two commands above use "RB_all_2008-03-26.gca" and "RB_all_withskull_2008-03-26.gca" which are freesurfer atlases for human brain. Here I have no clue how to create .gca files from my macaque images. I appreciate any help or insight. Thank you! Mahmoud

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