Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

Pass code
by Santiago Gómez 26 Mar '23

26 Mar '23

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images for my research project and a pass code is needed for this 7z archieve. Would you please send me the pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1MlcuMSSiFoTx0GjyrQW1D_iGKohpLuJFfWKiIEF3BcSo-…> ? I really appreciate it. Greetings, Santiago Gómez Castro, MD Neurosurgeon Universidad Nacional de Colombia Cel. +57 316 623 69 00 -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web http://secure-web.cisco.com/1GYOl7UuM7xf4ZhF71VSWMCVhFZCYuelWuXbjcGXGyzHOiT… <http://secure-web.cisco.com/1cYNL9a6ejl6w7JEp3F7zG0n1PylzIv5VwhJqbX6n3ZCuIX…>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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kvlThresholdImage: command not found
by Song, Xinrui 26 Mar '23

26 Mar '23

External Email - Use Caution Hello Dear Developers, I am trying to segment ex vivo hemisphere brains following instructions here "https://secure-web.cisco.com/1yI3dz-T0lQE-jN1p4p6MgEh8QOPQyERm9wL9X_vVhCt5v…". I was just proceeding to the Segment White Matter section and found that none of the kvl commands can be found in my installation. They are also not found in the freesurfer/bin folder. I searched the archive and found that there was one case that's very similar to mine, but it occurred back in 2012 and on a Mac distribution. (https://secure-web.cisco.com/1tVA2ZQl9_YrOUpNZqZ-IA4YxSqzjGL5Mp3wdVgTgftKi5…) Freesurfer version: freesurfer_ubuntu20-7-dev_amd64.deb Platform: WSL-Ubuntu on Windows.

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PETsurfer registration
by Douglas N. Greve 24 Mar '23

24 Mar '23

On the PETsurfer wiki, https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, I had recommended using mri_coreg to register your PET to the FS anatomical using the following command line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta This works well for PET scans that do not have much activity outside the head (eg, FDG and many neuroreceptor ligands). However, it can be inaccurate for other ligands that do have lots of uptake outside the head (eg, tspo, maybe tau). In these cases I now recommend using mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --ref nu.mgz --no-ref-mask This command will use the whole head MRI (nu.mgz) instead of the brainmasked MRI (brainmask.mgz); this will align better for these types of scans. This is now documented on the PETsurfer website. Remember, you should always check your PET-MR registrations manually. Sorry for any inconvenience this has created. best doug

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Re: [Freesurfer] SAMSEG in MS terminal error
by Cerri, Stefano,PHD 24 Mar '23

24 Mar '23

Hi Gabriel, These messages look like TensorFlow warnings. They just mean that you're running it on a system without GPUs. They should not stop the run. Is this the last message printed by run_samseg, or does the algorithm continues? Can you provide more details on when the run terminates? Stefano External Email - Use Caution Hi, I'm having difficulty with the command to assess WM lesion in MS, using the SAMSEG. I have already installed tensorflow and python3.9, however when typing in the terminal the command "run_samseg --input /home/username/data/t1.nii /home/username/data/flair.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/username/data/samsegOutput", this message appears: "2023-03-24 13:21:04.936769: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2023-03-24 13:21:04.936787: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7.2.0/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term" -- Att, Gabriel de Deus Vieira _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Postdoctoral Position in Cognitive and Translational Neuroscience at Brown University
by Elizabeth Sharp 24 Mar '23

24 Mar '23

External Email - Use Caution Postdoctoral Position in Cognitive and Translational Neuroscience at Brown University Area: Cognitive Neuroscience of Visual Memory, Aging, and Alzheimer’s disease Depts. of Cognitive, Linguistic, and Psychological Sciences (CLPS) and Psychiatry and Human Behavior Brown University We are seeking a highly motivated postdoctoral researcher to lead an NIH-funded project in the Laboratory for Cognitive and Translational Neuroscience directed by Dr. Hwamee Oh at Brown University. The project is to use fMRI and PET to study visual memory networks in healthy young, cognitively normal older adults, and older adults who are considered as preclinical Alzheimer's disease. Applicants with a Ph.D. degree in cognitive neuroscience, computational neuroscience, biomedical engineering, or a relevant field are encouraged to apply. Prior experience with human neuroimaging, a strong background in cognitive neuroscience and experimental design, and/or familiarity with programming in relevant languages (e.g., Python, MATLAB) are required. Applicants with experience with multivariate analyses on task-fMRI data are especially encouraged to apply. The successful candidate is expected to demonstrate communication skills, motivation and interest in the area of cognitive neuroscience of visual perception and memory, brain aging or Alzheimer’s disease, and the ability to independently develop research questions and work in collaboration with other team members. An expected start date is early summer or fall 2023. The position is primarily affiliated with Brown CLPS. Interested applicants should email a brief description of research background and career goals, and CV with a list of 3 references to Dr. Hwamee Oh at hwamee_oh(a)brown.edu. Contact Website https://secure-web.cisco.com/1534_IfZK4Xe7CtgB-h6v7DQVDNkwHRBS0xj2cNxbYGHZ3… Twitter @OhLabBrown -- Elizabeth Sharp Research Assistant Oh Lab Brown University

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SAMSEG in MS terminal error
by Gabriel Vieira 24 Mar '23

24 Mar '23

External Email - Use Caution Hi, I'm having difficulty with the command to assess WM lesion in MS, using the SAMSEG. I have already installed tensorflow and python3.9, however when typing in the terminal the command "run_samseg --input /home/username/data/t1.nii /home/username/data/flair.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/username/data/samsegOutput", this message appears: "2023-03-24 13:21:04.936769: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2023-03-24 13:21:04.936787: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. WARNING:tensorflow:From /usr/local/freesurfer/7.2.0/python/lib/python3.6/site-packages/tensorflow/python/compat/v2_compat.py:96: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version. Instructions for updating: non-resource variables are not supported in the long term" -- Att, Gabriel de Deus Vieira

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negative uptakes after GTM pvc correction
by Federica Di Antonio 24 Mar '23

24 Mar '23

External Email - Use Caution Dear experts, I report an answer you gave about some negative values avatar partial volume correction: "[...] Usually this only happens in small ROIs and/or low uptake regions. Why might the model not be perfect? It could be a number of things: 1. the MRI-PET registration is inaccurate 2. the MRI segmentation is inaccurate 3. the ideal segmentation is not reflected by the MRI segmentation (eg, one of the segmentations has a hot spot)" I wonder if it is possible for you to give me an hint about the reason why an inaccurate registration or segmentation can cause negative uptake values. At first sight it seemed intuitive to me, but on second thought that's not so obvious. I would be very grateful for any help! Federica Di Antonio

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Re: [Freesurfer] the virtual machine developer password RE: Password ubuntu password
by FS build 24 Mar '23

24 Mar '23

External Email - Use Caution Sent this again directly to your email. Please also check your spam/junk mail filters. - R. > On Mar 23, 2023, at 14:04, Zhao, Don <dzhao(a)messiah.edu> wrote: > > External Email - Use Caution > > The Freesurfer VirtualBox instructions state:“login as the user “developer” in the login menu. Get the password by sending an email request to the freesurfer help list.” > > Despite asking this question multiple times, I am still unsure of how to obtain the password. Can anyone provide assistance with this? > > Thank you in advance. > > Sincerely, > > Don > > From:Zhao, Don > Sent:Wednesday, March 22, 2023 2:00 PM > To:Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject:the virtual machine RE: Password ubuntu password > > “login as the user “developer” in the login menu. Get the password by sending an email request to the freesurfer help list.” > > Hi, freesurfer help list. > > May I have the password, please? > > Thanks, > > Don > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1-XqDz4WK1tf6mDhlS7ZpTZJj9SqZnaaQWC5dRd5x40Tn4…

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Password request for Ubuntu 18.04.06 compressed image with the FreeSurfer 7.2.0 release installed
by Rato Mendes, Pedro Fernando 24 Mar '23

24 Mar '23

External Email - Use Caution Dear Sirs, Following the instructions on VM_67 FreeSurferWiki page, I kindly ask you to please send me a valid pass code for the FS_7_2_0_Ubuntu_18_04_06.ova.7z archive. Thank you for your attention, best regards Pedro Rato-Mendes --*-- Pedro Rato-Mendes, PhD Technology Department CIEMAT - Ed.22 Avda. Complutense 40 28040 Madrid - Spain Tel: +34913466278 Fax: +34913466275

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Re: [Freesurfer] FreeSurfer Segmentation Fault
by FS build 23 Mar '23

23 Mar '23

External Email - Use Caution I setup the 7.3.2 release in an Ubuntu 20 VM by installing the .deb package available from under, https://secure-web.cisco.com/1Q2bcsIGqA45XXyvp1oUdk0FD9FaJp-NVNQeLjaHiqSpkZ… The tutorial data I tested is from 2020 (not 2019), but that might not matter for that file (whose date is from 2018). I also use some soft links from $HOME to point to the freesurfer distribution and the tutorial data subdirectory, but again don't see that should make a difference. But freeview does open that individual file in my VM setup. if you want to try the same copy of the tutorial data I used you can get it from https://secure-web.cisco.com/1p3t4GUS5V08DKAzGkEoAeSvD3K-WIb6nplLAYdQGXnfAh… You can see the terminal session in the attached screenshot, freeview_ub20,jpg If you did not use the .deb package for the install of 7.3.2, then I would try that. Otherwise there may be something going on with your shell environment. There may be more info listed about the crash in /var/log/messages if you look there just after the crash. - R.

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Freesurfer March 2023