Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

IP Problems
by Alison McDonnell 13 Oct '21

13 Oct '21

External Email - Use Caution I was having some trouble with Freesurfer on a windows computer and was wondering if you had any ideas. I was able to download and install it but when I got to the end to run it I got the error message to do with the IP address, the same as the one shown in the screenshot below. The instructions said this could happen so wasn't worried and did what they said but the error happens every time I logout and log back in. The freeview program also doesn't actually run but seems to try to load and no errors come up when I try run it so I think I might just not be fixing the IP problem. [image: image.png]

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Re: [Freesurfer] Segmentation fault (core dumped) of freeview
by fsbuild 13 Oct '21

13 Oct '21

External Email - Use Caution Hello Yuhui, Did you try something like the following (from https://secure-web.cisco.com/1hub7Psr57JCR6YgoGWEJLmEuz6voF9O_4wwW1Ngq-Krek…) to set FREESURFER_HOME (?) and then after source'ing the shell setup script you should of seen output like ... $ export FREESURFER_HOME=/your_path_to/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /home/tester/freesurferFSFAST_HOME       /home/tester/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/tester/freesurfer/subjectsMNI_DIR           /home/tester/freesurfer/mni $ which freeview/your_path_to/freesurfer/7.2.0/freeview … set TUTORIAL_DATA … I would try just typing freeview on the command line to test that it brings up an empty window before trying to run any of the tutorial commands with it, $ freeview - R. On Oct 12, 2021, at 22:42, Yuhui LIANG 梁玉慧 <liangyuhui(a)westlake.edu.cn> wrote:        External Email - Use Caution                External Email - Use Caution        Hello,As a beginner, I am trying to run freeview -v using tutorial_data by the code below.freeview -v \good_output/mri/T1.mgz \good_output/mri/wm.mgz \good_output/mri/brainmask.mgz \good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \-f good_output/surf/lh.white:edgecolor=blue \good_output/surf/lh.pial:edgecolor=red \good_output/surf/rh.white:edgecolor=blue \good_output/surf/rh.pial:edgecolor=red I am getting an error :Segmentation fault (core dumped)but it did not produce CORE file. And I've downloaded the tutorial data set before begin and I am sure that set the TUTORIAL_DATA environment variable properly as specified on the tutorial data page. I am using freesurfer version 7.2.0 in CentOS 8. Any advice would be appreciated! Thanks, Yuhui_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1Thxeq5mfyjHL_ecNgfklwIAfLQXmU16VfwPdyUKAEKqI3tHHfJBOS99IgKieVMP1yJHqdMyYdM8YKNO41VpZxyy8QefzmhvAveAr7KCEFmfqRMhDCLZBp4cDP8V_Q9AhKdxDr5U0wEeEje5Nj9HXVy4Q3vemfAVWo1jwgjJTjbVzGuh82uuVinDziFut_t5uJ1e9nMgXnk2bHv7F49TbGgLvplUj2Bj7osfbpUAqQ0MYQZmw2rChHKEqez3A1ywYFPsmGYC3guJm5PmQ7h13lw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Segmentation fault (core dumped) of freeview
by Yuhui LIANG 梁玉慧 12 Oct '21

12 Oct '21

External Email - Use Caution Hello, As a beginner, I am trying to run freeview -v using tutorial_data by the code below. freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red I am getting an error :Segmentation fault (core dumped) but it did not produce CORE file. And I've downloaded the tutorial data set<https://secure-web.cisco.com/1YhwP8bFwqbQw8ArjPIWKZBPJes6m8JxvN_roH8NEcnLfd…> before begin and I am sure that set the TUTORIAL_DATA environment variable properly as specified on the tutorial data page. I am using freesurfer version 7.2.0 in CentOS 8. Any advice would be appreciated! Thanks, Yuhui

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Open positions at The Ohio State University: Post-dococtoral Researcher, Psychometrician, & Study Coordinator
by Teng, James 11 Oct '21

11 Oct '21

External Email - Use Caution The Clinical Neuroscience Lab, in the Department of Psychology, within the College of Arts and Sciences, seeks a Post-Doctoral Researcher (R29059), a Psychometrician (R13824), and a Study Coodinator (29068) to join our team. The Clinical Neuroscience Lab is directed by Dr. Ruchika Prakash, and the laboratory is funded by the National Institute on Aging to conduct a randomized controlled trial of mindfulness meditation for older adults in the Columbus community. The lab recently received additional funding to increase the representation of Black, Indigenous, and/or People of Color in our clinical trial. We are excited to receive this funding, and we hope to find a candidate who is passionate about working with diverse communities and individuals. Apply online at: https://secure-web.cisco.com/11XZ7GSpquo2K34Cy2WyF2fIiLSV2uXiUNvLonCYJRP5v6… under the respective job listings Post-Doctoral Researcher (R29059), Psychometrician (R13824), and Study Coodinator (29068), and submit a CV, a brief statement of your research interests, your expected date of availability, and the names and contact information of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu. Lab Website: https://secure-web.cisco.com/1br5PNyboP4J53ZddAEBfrlv5QBGhIfyia8PupfmAqaxSL… To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status.

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error using mri_convert
by Rizzo, Nolan W 11 Oct '21

11 Oct '21

External Email - Use Caution Hello FreeSurfer developers, I am attempting to use mri_convert to convert DICOM files to a NIfTI file. The DICOM images were obtained from a Siemens 3T Prisma scanner with VE11C software version. When mri_convert is run to convert the .dcm files to .nii , an error occurs that displays "bad fd number". I believe the problem occurs when mri_convert is trying to decompress the new JPEG format of the DICOM files. I have listed the FreeSurfer version and OS that I used below. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Ubuntu 16.04 This error did not occur when running mri_convert on the Mac version of FreeSurfer using OS Mojave. The same DICOM files (as above) were used. mri_convert ran without error and produced the .nii file. Thank you.

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Question about fsaverage
by Dongyue Zhou 11 Oct '21

11 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'. I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices. Is there any way I can get annot for this file in one sub?

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Question about fsaverage
by Dongyue Zhou 10 Oct '21

10 Oct '21

External Email - Use Caution Dear FreeSurfer experts: I want to know cortical thickness in this file 'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard space or in native space. Is not the common coordinate system the same as standard space? And if mean ROI CT measures computed by this file is the same as that computed by file 'subjectname/stats/?h.thickness'. If not,I want to use fsaverage file to compute mean CT measures of each ROI,how should I locate each region?

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Faculty positions at Bilkent University
by Burcu Ayşen Ürgen 10 Oct '21

10 Oct '21

External Email - Use Caution Dear colleagues, Bilkent University has 3 open faculty positions whose details are provided in the links below: *Open-Rank Position at the Department of Psychology, Bilkent University <http://secure-web.cisco.com/1CBqMH2JwP6VpxGPSQ2fHpMHy2LrnuWlgqgU4BIzznq158h…>**Instructor Position at the Department of Psychology, Bilkent University <http://secure-web.cisco.com/1zzq8SzN6sb5MNAZIAqG2QGQ-X7Rcx-WGxTkSG0U8Q5fe7N…>* *Instructor Position in Clinical Psychology at the Department of Psychology, Bilkent University* <http://secure-web.cisco.com/13cr6VZPX_m3HoJr7YJojYmAJf-1o94zUIt3T94wiIPjdLh…> Best, Burcu -- Burcu Ayşen Ürgen, PhD Assistant Professor Department of Psychology Interdisciplinary Neuroscience Program Aysel Sabuncu Brain Research Center National Magnetic Resonance Research Center Bilkent University 06800, Bilkent, Ankara, Turkey Email: burcu.urgen(a)bilkent.edu.tr Website: http://secure-web.cisco.com/1hAG7qa7TBljujr0-X4ey49D3mc8zT6LU6tB2fC6Yo1cVeq… Lab: http://secure-web.cisco.com/1eDYIkzVTvrjlW2_2UoP-GIY_kcwVXVlGGclZJr-iMYDkTh… Tel: +90 312 290 30 91 or +90 312 290 1807

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Freesurfer version help
by Annalisa Lella 09 Oct '21

09 Oct '21

External Email - Use Caution Hi, I was wondering if you could help me or give me more information. I have pre-processed my MRI data using FreeSurfer version 7.0, which has been recalled. I used the same version for the thalamic segmentation. I have elaborated my data one year ago. Do I have to pre-process all my data again? I randomly segmented few subjects with versions 6.0 and 7.2 and I implemented a visual quality check but it seems to me that the images segmented with version 7.0 are good. I runned also t-tests between the extracted cortical volumes of the three versions and there are overall few differences across the versions. Where could I see if my data are not good? Which are the effects of the bug in version 7.0? Thanks a lot for any help you could give to me! Best regards, Annalisa Lella

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individual analysis and visualization
by Zeng, Qi 08 Oct '21

08 Oct '21

External Email - Use Caution Hi Experts, If I want to analyze and visualize baseline and follow-up for an individual subject's change (before-after & after-before). Should I treat it as a cross-sectional analysis for a group analysis? Best, Zeno

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Freesurfer October 2021