Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

Re: [Freesurfer] Freesurfer issue
by fsbuild 11 Aug '23

11 Aug '23

External Email - Use Caution  Please try the following, … open a new terminal and run the bash shell … I am cd’d to /tmp though it should not matter ... $ cd /tmp$ bash The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://secure-web.cisco.com/1G4FPb9n4t6EAd65_hmtnkfEITITNTkf9OQlUdDQs6VJF-… … check the version of Quartz by starting an xterm.  When the xterm window opens check the version from the upper left hand corner XQuartz application pull down menu and check what “About X11” reports.  In the example below, Quartz 2.8.5 is running on a late 2019 Intel MacBook Pro with MacOS 12.6.7 (Monterey) installed …  Mac:/tmp> which xterm /opt/X11/bin/xtermMac:/tmp> xterm & … check you have Quartz 2.8.2 or later and then quit the xterm window … … copy your license.txt file into your home directory.  For example if you downloaded your license attached to the email notification into your Downloads folder, then copy it from there into $HOME … Mac:/tmp> cd $HOME Mac:~> cp -p -f  Downloads/license.txt . … set the environment variable FS_LICENSE to point to the license file … later you can put this in your shell init file to be the default when you launch a new terminal window with your default shell …  Mac:~> export FS_LICENSE=$HOME/license.txt Mac:~> head -1 $FS_LICENSEyou(a)somedomain.com                   <— email you used to register for the license … setup the freesurfer environment … Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.4.1 Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.4.1 FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects MNI_DIR           /Applications/freesurfer/7.4.1/mni … first check freeview with no arguments opens an empty window … Mac:~>  which freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~> freeview … close the window and try to open a volume or surface ... … check the volume file exists … Mac:~> ls -l $SUBJECTS_DIR/bert/mri/T1.mgz -rwxr-xr-x  1 root  wheel  4502402 Jul 13  2021 /Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz* … try opening the volume file …Mac:~> freeview $SUBJECTS_DIR/bert/mri/T1.mgz The above works on the Mac configuration listed above. - R.  On Aug 11, 2023, at 18:59, Irakli Kaloiani <ikalo(a)stanford.edu> wrote:        External Email - Use Caution        Dear Freesurfer team,Several members of our lab tried setting up Freesurfer (V.7.4.1) and about 5-6 people have encountered the same problem (all of the on macOS) of freeview crashing when we are trying to load the T1 from the folder bert>mri>T1. We already have license file placed in an appropriate folder.Additionally, there’s an issue with XQuartz (V.2.8.5) when I am trying to run xclock in terminal – “Error: Can't open display:”Do you know what could be an issue? Google and stackoverflow wasn’t useful.Your advice would be greatly appreciated,Thankfully,Irakli    Irakli Kaloiani, M.D.TMS LeadBrain Stimulation Lab, Stanford UniversityDepartment of Psychiatry and Behavioral SciencesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ZkGWHgZJw-3zmLYe8yrmEG28cyI9K8rL_avCqm… 446 - 1596 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer issue
by Irakli Kaloiani 11 Aug '23

11 Aug '23

External Email - Use Caution Dear Freesurfer team, Several members of our lab tried setting up Freesurfer (V.7.4.1) and about 5-6 people have encountered the same problem (all of the on macOS) of freeview crashing when we are trying to load the T1 from the folder bert>mri>T1. We already have license file placed in an appropriate folder. Additionally, there’s an issue with XQuartz (V.2.8.5) when I am trying to run xclock in terminal – “Error: Can't open display:” Do you know what could be an issue? Google and stackoverflow wasn’t useful. Your advice would be greatly appreciated, Thankfully, Irakli Irakli Kaloiani, M.D. TMS Lead Brain Stimulation Lab, Stanford University Department of Psychiatry and Behavioral Sciences http://secure-web.cisco.com/1RHVnzkdkghVD88sQKgeeHZj-1_DBo5FH8k5JPRqJPKO4i0… (415) 446 - 1596<tel:650-800-6920>

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Re: [Freesurfer] ln: failed to create symbolic link 'file': Operation not supported error
by fsbuild 11 Aug '23

11 Aug '23

External Email - Use Caution Hello Gizem, Are you by any chance running Ubuntu Linux through WSL or a VM on a Windows machine - AND/OR  - trying to write your data from Ubuntu linux to a mounted NTFS file system on a Windows machine?   The Windows file system does not support symbolic links and so you need to set SUBJECTS_DIR to point to path on a Linux file system.  I am not aware of linux OS file systems that do not support symbolic links. - R.

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T2 FLAIR images
by Alan Francis 11 Aug '23

11 Aug '23

External Email - Use Caution Good evening all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 #-------------------------------------------- #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1 --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375, 0.9375, 1.2 *error: MultiRegistration::loadMovables: voxel size is different /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz.* Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 recon-all -s NCANDA_S00042 exited with ERRORS at Mon Aug 7 16:06:29 CDT 2023 -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Installation tensorflow: protobuf requires Python '>=3.7' but the running Python is 3.6.8
by Jong, J.J.A. (Joost) de 11 Aug '23

11 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I would like to run samseg with the lesion module, hence samseg is asking to install Tensorflow using the following command: fspython -m pip install tensorflow==1.13.1 However, when execute the command, I get the following error: protobuf requires Python '>=3.7' but the running Python is 3.6.8 The problem persists when create a conda environment and try to install tensorflow there. I cannot seem to work around this problem, as fspython version seems to be 3.6.8. Why does FreeSurfer come with a Python version that conflicts with a protobuf version required to install tensorflow 1.13.1? Looking forward to your ideas/suggestions! Best regards, Joost de Jong Maastricht UMC+, The Netherlands FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b Platform: CentOS Stream release 8 uname -a Linux radstation27.prd.corp 4.18.0-408.el8.x86_64 #1 SMP Mon Jul 18 17:42:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux ___________________________________________ Dr. Ir. Joost de Jong Senior Researcher Department of Radiology and Nuclear Medicine Visiting address: P. Debyelaan 25 | 6229 HX Maastricht Location: 4th floor, Room 4.H1.002 Postal address: Postbus 5800 | 6202 AZ Maastricht Maastricht UMC+ is a commercial name of azM, Chamber of Commerce no.:14124959 E e-mail address: j.dejong(a)mumc.nl | T +31 (0)43 38 74871 I http://secure-web.cisco.com/1TpM-pyj3jiJroVpfVeteQX14SCBG38j6yjGHU417S98I6E…<http://secure-web.cisco.com/1QKGqMChi0EuhQOKcM2h6MgZEowPxfNXfjZnF63KheUmVyX…> | http://secure-web.cisco.com/1OWWDYyMq9U6pHTPuxlmvarkGZroDverVyUC-msNiVy-hy6…<http://secure-web.cisco.com/1M1zOL-XvgT6vJF2ypQQAMXmM6wb82kiy6zYURLqTj3Gpad…> Follow us on Twitter<https://secure-web.cisco.com/1_xhiCTMlQOowUfDjYP14RRMxfPgUPnZOckHkdvvZtSD3l…>, Facebook<https://secure-web.cisco.com/1iZHQnMegyxXeanDho81aAKRFgmFeaf4vvT2rMQKdMjvAR…> and LinkedIn<http://secure-web.cisco.com/1YweY1DY29HflopcYocSi02MCLHl2sA6mPcIrSXx-EbYH1p…> ________________________________ This email and any attachments may contain confidential or privileged information and is intended for the addressee only. If you are not the intended recipient, please immediately notify us by email or telephone and delete the original email and attachments without using, disseminating or reproducing its contents to anyone other than the intended recipient. The Maastricht UMC+ shall not be liable for the incorrect or incomplete transmission of this email or any attachments, nor for unauthorized use by its employees. ________________________________

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Question about glmfit results and visualization by using Freeview
by inbal paran 11 Aug '23

11 Aug '23

External Email - Use Caution Dear FreeSurfer developers, Thank you for your response to my previous questions, I have a few more (I'm inexperienced with both Freesurfer and Linux): 1. Can I visualize my results after running mri_glmfit by using Freeview, such that the image shows cortical brain regions as well as subcortical brain regions on both hemispheres? If yes - how can I do that? 2. Is there a text file of the glmfit results that includes the correlation parameters, cluster size, significance/p-values? If yes - where can I find it? If not - how can I generate one? Thank you very much Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1YZJEd4xAGXQnv0pIXxLgi_JVIUWn7hQJs_Lvjrak6I2_f9…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

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RA Position for Human Intracranial EEG Lab
by Winfield, Jalen 11 Aug '23

11 Aug '23

External Email - Use Caution Dear all, The human intracranial EEG Laboratory at The Feinstein Institutes for Medical Research - Hofstra Northwell School of Medicine in New York is looking for a research assistant with earliest start date in October 2023. 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 macro-scale 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 responsibilities will include assisting with the collection and analysis of the aforementioned data, project management, assistance with grant applications and progress reports, help with analysis of neural and imaging data using existing scripts (Matlab, Python), further development of those scripts (depending on coding and signal processing proficiency), and helping to present lab findings at conferences and in journals. The relative weighting of responsibilities can be adjusted depending on the interest of the applicant. If there is interest, the RA will have a scientific project with dedicated time to work on. Past research assistants have presented their work at clinical and basic research conferences, co-authored 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) - 2-year commitment - Experience with at least one programming language (MATLAB, R, or Python) Desirable: - 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<mailto:sbickel@northwell.edu>). 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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Fundi of Sulci
by Bluye Demessie 11 Aug '23

11 Aug '23

External Email - Use Caution Dear FreeSurfers, I am hoping to do an analysis of DTI metrics within the WM at the fundi of sulci. I am working with FreeSurfer v7.4.1 and want to use the ?h.curv to isolate the bottom of the sulcus based on the most positive curvature. Since ?h.curv is not a surface but rather a scalar field, is it possible to map ?h.curv to a volume in NIfTI format that can be overlayed on the original input NIFTI file with T1-weighted images used to produce the curvature map? Sincerely, Bluye

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mri_segstats --avgwf output question
by Lara Foland-Ross 11 Aug '23

11 Aug '23

External Email - Use Caution Hi there, I'm running mri_segstats on a collection of clusters resulting from a statistical analysis. My command line usage is as follows: mri_segstats --i lh.fwhm10.thickness.mgh --avgwf clusterAverages.txt --seg cache.th13abs.sig.ocn.mgh The results from my statistical analysis in the case of left hemisphere thickness shows 4 clusters that are significant in total, but the clusterAverages.txt contains a total of 5 mean thickness values per subject. This extra value is also reflected in other analyses in my dataset (for other hemisphere and for thickness, area and volume). Is the extra value listed per subject a global mean of some sort? If so, is it the first column of values or the last? Thank you, Lara

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Freesurfer Virtual Machine Password Request
by Gabriel Varga 11 Aug '23

11 Aug '23

External Email - Use Caution Hi, I'm looking to get the virtual machine password as I have been trying to get freesurfer to run on my windows computer. Please let me know if you need more information from me before sending, I'd be happy to provide it. Thank you! Regards, Gabriel Varga

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