Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Freesurfer VM 7zip passcode
by Mikolaj Pawlak 04 Jul '22

04 Jul '22

External Email - Use Caution Hello, I would like to ask for the passcode for the VM file containing FS7.2 thanks, Mikolaj Pawlak

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Freesurfer VM password
by Zixuan Lin 03 Jul '22

03 Jul '22

External Email - Use Caution Hello! I just downloaded the FS_7_2_0_ubuntu_18_04_06.ova.7z and would like to see if I can get the password to unzip this VM? Thanks a lot, Zixuan.

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trac-all -prep -c ERROR
by Salar Dini, Elaheh 03 Jul '22

03 Jul '22

External Email - Use Caution Dear experts, I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I get the following error in -prep step: ((INFO: Distances between consecutive points in test subject's space are 10 13 12 13 13 12 WARN: Could not find satisfactory control point fit - try 17034 Writing output files to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_* Writing spline volume to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz Segmentation fault (core dumped) Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022)) I am attaching the log file as well: https://secure-web.cisco.com/1SmnY7WYnV1XRZV1hzFK0-fljtz5hTgSEDuVurOZOZqB22… On a quick look, aparc+aseg seems to be properly done. Will you please help me to troubleshoot this if possible? Thank you, Ela

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segmentation corpus callosum
by Mostafa Fakhri 03 Jul '22

03 Jul '22

External Email - Use Caution Hello to all, I was wondering if I could create a binary mask of corpus callosum from T1w images in subject space with FS. Thanks for the help! Mostafa

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Pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Sharma, Maya 03 Jul '22

03 Jul '22

Hello, I am downloading Freesurfer on my Windows device; may I please have the pass code to expand the archive FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you kindly

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infant freesurfer crash
by Knut J Bjuland 02 Jul '22

02 Jul '22

External Email - Use Caution I am able to run infant freesurfer on my local pc but when I run on a cluster I get segmentation error when running sscn_skullstrip. Segment error in $ sscnn_skullstrip -i /cluster/projects/nn9208k/007_fs/work/mprage.nu.conf.nii.gz -o /cluster/projects/nn9208k/007_fs/work/sscnn -c t1w Segmentation fault (core dumped) How can I provide more information, I have enable 24 Giga byte of ram. Knut Jørgen Bjuland

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help troubleshooting lta_convert error
by Megan Schendel 01 Jul '22

01 Jul '22

External Email - Use Caution Hi all, I had a working distribution on an old system a few weeks ago, but now I'm getting an error. Can anyone offer any troubleshooting ideas? I am working on a shared server with a freesurfer distribution that I own. Here is some system info: [mschendel@earth scripts]$ lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.7 (Final) Release: 6.7 Codename: Final On the command line, the error looks like this: lta_convert: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by lta_convert) lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by lta_convert) lta_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.19' not found (required by lta_convert) lta_convert: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by lta_convert) The recon-all.log file contains the following: Fri Jul 1 11:08:24 MDT 2022 cd /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis/M87124539 setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer//bin/recon-all -all -i /export/research/archive/human/dicom/prisma/dquinn/navigate_20673//M87124539/Study20210623at161830/mprage_5e_32ch_RMS_0003/SerieMR-0003-0001-1.dcm -s /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis//M87124539 -openmp 8 subjid M87124539 setenv SUBJECTS_DIR /export/research/analysis/unm_psych/dquinn/Navigate_20673/MEG_source_analysis FREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer/ Actual FREESURFER_HOME /export/research/analysis/human/jstephen/shared/programs/freesurfer_7.2/freesurfer build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Linux earth.mind.unm.edu 2.6.32-573.26.1.el6.x86_64 #1 SMP Wed May 4 00:57:44 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited ######################################## program versions used 7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) ERROR: Executable 'lta_convert -all-info failed! Is it missing from the distribution?' MEG Technician Pronouns: she/her The Mind Research Network 1101 Yale Blvd. NE Albuquerque, New Mexico 87106

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Research Assistant Opening at Human iEEG Lab in NY
by Tostaeva, Gelana 30 Jun '22

30 Jun '22

External Email - Use Caution Hello all, Please circulate this opportunity to any interested parties. Sorry for cross-posting. Thank you! ------------------------------------------- The human intracranial EEG Laboratory at The Feinstein Institutes for Medical Research – Hofstra Northwell School of Medicine in New York is looking for one research assistant with earliest start date in July 2022. The successful candidate will help with the lab’s research into (1) improving the identification of functional and pathological brain regions in individuals suffering from epilepsy, (2) the neural mechanisms of cognition, and (3) characterization of macroscale human brain networks. The lab works exclusively with patients being evaluated for epilepsy surgery using methods such as invasive stereo EEG and electrocorticography recordings (iEEG, ECoG), anatomical MRI, fMRI, DTI, and direct electrical brain stimulation. The position is computationally focused, and responsibilities include analysis of neural, imaging, and behavioral data using existing scripts (Matlab and Python), further development of analysis scripts (depending on proficiency with coding and signal processing), and database managing. However, responsibilities will also include assisting with the collection and analysis of the aforementioned data, project management, assistance with preparing progress reports and grant applications, and helping to present lab findings at conferences and in journals. The relative weighing of responsibilities can also be adjusted depending on interest of the applicant. In addition, if there is interest, the RA will have her/his own scientific project with dedicated time to work on it. Past research assistants in the lab have presented their work at clinical and basic research conferences, co-authored lab publications, and are working on first author publications. They have gone on to medical schools or PhD programs after spending 1-3 years in the lab. This unique position will expose the successful applicant to basic and clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. The location of the institute allows living either in the suburban neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees also commute from Manhattan. It is a great opportunity for recent post-bacs interested in medical school or graduate school in neuroscience/biomedical engineering. ------------- Qualifications ------------- Minimum: - B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, biomedical engineering, computer science, physics) - 1 year commitment - Experience with at least one programming language (MATLAB, R, or Python) Desirable: - 2-year commitment preferred - Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data - Previous experience working with patients - Previous work in a research laboratory that shows evidence of independent scholarship, problem solving, and motivation For more information about the position please send your CV along with your questions to Dr. Stephan Bickel (sbickel(a)northwell.edu) and Dr. Ashesh Mehta (amehta(a)northwell.edu) We are looking forward to hearing from you! The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or 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 communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Re: [Freesurfer] Tksurfer Error
by fsbuild 29 Jun '22

29 Jun '22

External Email - Use Caution The tksurfer command is deprecated/no longer supported. You could try using freeview directly or run tksurferfv, which may take the same options as tksurfer but run freeview to display things. - R.. On Jun 29, 2022, at 16:33, Rachel Wagner <rwagne2(a)uwo.ca> wrote:        External Email - Use Caution        Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find a usable init.tcl in the following directories:    /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4   This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary"Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories:./library./tix8.1./library./tix8.1/usr/pubsw/packages/tcltktixblt/current/lib/tix8.1  How can I fix this error? Thanks, Rachel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Fwd: Pass code to expand archive for VirtualBox
by Cody Slater 29 Jun '22

29 Jun '22

External Email - Use Caution Hello, I am following the instructions to install the VirtualBox for Freesurfer 7.2.0 and would like access to the code for expanding the archive. Regards, Cody Slater

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Freesurfer