Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Question about running recon-all with deface
by Mishra, Virendra 10 Dec '15

10 Dec '15

Hello, We are currently in the process of analyzing some data that was defaced using mri_deface command of freesurfer. This defaced data was then used as an input to recon-all and the volume and thickness was computed. These results were then compared against the same subject's recon-all with the face but with and without the deface flag within recon-all. All of the steps were done on version 5.3.0. We have got some differences and we are unable to explain why. Some of the regions have error greater than 20% when the input was a defaced brain. We would appreciate if you could advise as to how to approach to the same results as we were running the data with the face . To summarize: (The commands are not precise below but we ensured the commands are run correctly per the command help) 1) Step 1: mri_deface -i original_T1 -o deface_T1 2) Step 2: recon-all -i deface_T1 3) Step 3: recon-all -i original_T1 -deface 4) Step 4: recon-all -i original_T1 5) The results from Step 3 is exactly equal to Step 4 6) The results from Step 2 and Step3/4 have errors >20% in certain regions. 7) Step 1-4 are done with version 5.3.0 Any response will be greatly appreciated. Thanks Regards Virendra =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Shifted surface after gyrification index is calculated
by Chris Holdgraf 10 Dec '15

10 Dec '15

Hey Freesurfer folks - I'm looking into using Freesurfer for doing electrode reconstruction / co-registration in electrocorticography. We're making good progress on figuring out recon-all for surfaces and doing co-registration to CTs. However, I think I've encountered a strange bug. I'm trying to create a smoothed pial surface so that I project electrodes onto this surface. The code seems to run correctly, however, the smoothed surface looks translated relative to the original pial surface that it was created from. For example, see this issue I opened on github: https://github.com/aestrivex/gselu/issues/7 Anyone have an idea why this is happening? I'm not sure why the pial surface would be correct, while the smoothed surface would be shifted. Chris -- _____________________________________ PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/> Editor and Web Director | Berkeley Science Review <http://sciencereview.berkeley.edu/> _____________________________________

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reg-feat2anat error ("mri_convert ERROR: could not determine file")
by Emily Coffey 10 Dec '15

10 Dec '15

Hello, I am having a similar problem to that posted several times previously. I get an error when running reg-feat2anat to register FSL feat files to the freesurfer reconstruction, see: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038437.html because the subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii file does not seem to make itself. I'm wondering where I can find an active link to an updated reg-feat2anat, as all the links I find in threads are not working. I did find a potential workaround: if I create the /mri/tmp directory and convert the .mgz file from the freesurfer output to .nii here, as explained on this website (http://wikis.la.utexas.edu/imagelab/book/how-convert-mgz-structural-files-n…) I can create the missing nii file and rerun the registration, however, I'm uncertain about the orientation parameters as although the orientation of the nii matches that of my original T1, the resulting registration in freesurer is nonsense. Example of the command I am using to manually convert the .mgz to nii: mri_convert --in_type mgz --out_type nii subjectsfreesurferfolder/mri/brainmask.mgz --out_orientation RAS subjectsfeatfolder.feat/reg/freesurfer/tmp/refvol.fslregister.nii Any suggestions on either the updated file location or the workaround much appreciated! Notes: I am running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 On Linux: Ubuntu 12.04.5 LTS Emily

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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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Freesurfer December 2015