Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

Applying Wang Atlas to Group Analysis Results in FreeSurfer
by Sujeevini Sujanthan 19 Jan '24

19 Jan '24

External Email - Use Caution Hi, I would like to apply the wang atlas over the group activation maps produced from Freesurfer analysis. I would appreciate any guidance/instructions you can offer for how I can do that. Thank you for your time!

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EasyReg question
by Èlia Pedregosa 19 Jan '24

19 Jan '24

External Email - Use Caution Dear Juan Eugenio Iglesias, We are a biomedical engineering company (BIOREM) in Barcelona, and we are collaborating in a research and innovation project with the University of Barcelona. For this project we use EasyReg to do brain registrations. However, we have some problems with the necessary memory to run the program. In that sense, we ask you which computational requirements we need. If it is possible, could you provide us this information? Thanks, best regards. Èlia Pedregosa Sandoval BIOREM_biomedical engineering Madrazo 68, bxs. 08006 BARCELONA Telf. 934 186 129 http://secure-web.cisco.com/1_MkzRbqyiH66KINd6uLPW_76jujv3qAzV1ApABqrJsjeA5…<http://secure-web.cisco.com/1hwvnraVglmADsDEbkSqMeXsjPrZJpioumEzOxIWUrmWh2G…> [cid:f6917007-7636-4b37-be0a-010ab3bd281d]<http://secure-web.cisco.com/1hwvnraVglmADsDEbkSqMeXsjPrZJpioumEzOxIWUrmWh2G…>[cid:c6b9a427-fbb1-4f20-986e-499840b7bfe5]<https://secure-web.cisco.com/1usD7oypvISKxz1aQD5yWVstXVJ4ILSB42PJyvh6B-AJ8H…>

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Issue with mri_brainvol_stats for only some participants
by Carly McIntyre-Wood 18 Jan '24

18 Jan '24

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Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields
by Heese, E. van (Eva) 18 Jan '24

18 Jan '24

External Email - Use Caution Hi all, Thanks again for your help. We fixed the issue by adding user write permissions for the owner-user in the installation folder (note that the owner of the file in the installation folder is different from the users that we used for testing). : -rw-r--r--. 1 admin admin 366711 Sep 21 2017 /installationfolder/7.3.2-centos8_x86_64/average/HippoSF/atlas/AtlasDump.mgz The fix was necessary for the other AtlasDump.mgz files. Best, Eva ______________________________________________________ AmsterdamUMC disclaimer : http://secure-web.cisco.com/1wlx9tXYYUIMj_Rg1KZxU9HYTynqYvQ9dJZEYbomVrvzBlz…

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Ex-vivo adult brain MRI segmentation and surface analysis
by K Eswar 18 Jan '24

18 Jan '24

External Email - Use Caution Dear FS community I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. I have recently come across a paper on MRI segmentation using a function called- samseg. From the webpage( https://secure-web.cisco.com/1AJdw_iZ93Ctl2bXUM-tS9sQoJ_9a6-0RHBNEGqz7c8Pz8…) I realized that there is a different approach altogether to processing these fixative brains. However, as a first step, when I tried the samseg function, I noticed that the function exited with errors. The steps where it fails are: Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Read mesh collection: /home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Killed I am using the Ubuntu 22.04 version with RAM 32GB Freesurver version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 I would greatly appreciate it if you could help me with MRI segmentation and cortical surface analysis on these brains. Thanks for your time and consideration. Regards K Eswar Project Scientist Sudha Gopalakrishnan Brain Centre IIT Madras, India

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T1map processing error
by Maksim Slivka 18 Jan '24

18 Jan '24

External Email - Use Caution Dear FS community, Recently our lab started collecting 3D-QALAS (Cho et al., 2023). Using this method, a quantitative T1map was constructed. Trying to process this map, FS (v7.1.0) recon-all would output the following error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping I would like to ask if anyone here has experience in processing quantitative T1maps with FS? Did you also run into that error? Were you able to solve it? I am looking forward to hearing from you. Best regards, Maksim Slivka Head engineer Center for Lifespan Changes in Brain and Cognition (LCBC) Department of Psychology University of Oslo POB 1094 Blindern 0317 Oslo Norway

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recon-all errors (cannot execute binary file +
by 윤혜정 16 Jan '24

16 Jan '24

External Email - Use Caution Good day. When I run recon-all for my nii files I get either one of the following error messages: 1. ERROR: could not configure recon-all parameters Killed 2. ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0 Or 3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the developer cannot be verified. mac OS cannot verify that this app is free from malware. I googled the third error message and tried "Allow anyways" from the privacy setting. Then the next message pops up, then the next and the next. Could you please help me to understand the cause of the above 3 error messages? I tried to redownload freesurfer as well as python but none worked. Thank you in advance. Best, Alice

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Re: [Freesurfer] recon-all errors (cannot execute binary file +
by fsbuild 16 Jan '24

16 Jan '24

External Email - Use Caution It looks like you did not use the .pkg file installer to install Freesurfer on the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to use as FREESURFER_HOME.  The installer should ensure the privileges should be correct to run commands.   There are several 7.X freesurfer releases, but the latest release is 7.4.1 and you can download it via the link, e.g., https://secure-web.cisco.com/1bTTDiznaFEJgJPDoi2yskrFqRdt_lNsr8LZ0PFjdBlc19… I would first remove what you have on your system from the terminal window with, $ sudo rm -rf /Applications/freesurfer Then in a Finder Window navigate to the Downloads folder (or to wherever you downloaded freesurfer-macOS-darwin_x86_64-7.4.1..pkg).  You should be able to RIGHT CLICK on that file, select open with the default pkg installer, and then enter your password etc. to install it.  Right clicking should bypass having to do some of the security exemptions in system preferences. Once the install is complete, setup the Freesurfer environment in the terminal window, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ 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 You also need a license file, license.txt.  Once you complete the license request form at https://secure-web.cisco.com/1Svw39fuKLV2rL8mAOfpPDMZrLLodE_ScR0sKC… will receive a file “licesne..txt” via the email address used in the form.   Download/copy the license.txt file to your machine from the email. If your home directory is for example /Users/hyejung then you will see the following in the terminal window, $ cd$ pwd/Users/hyejung$ echo $HOME/Users/hyejung … if you downloaded license.txt into your Download folder ... $ cd Downloads$ ls license.txtlicense.txt$ cp -p -f  license.txt  $HOME/.$ cd $HOME$ ls license.txtlicense.txt You could also use the Finder to navigate and drag/drop the license.txt into your home directory.   Once it it there, set the environment variable FS_LICENSE so freesurfer commands will find the license when they run, $ export FS_LICENSE=$HOME/license.txt Then it should work to run freesurfer commands from the terminal window including freeview. - R. On Jan 16, 2024, at 20:47, 윤혜정 <hyejung7890(a)amc.seoul.kr> wrote:        External Email - Use Caution        Good day.When I run recon-all for my nii files I get either one of the following error messages:1. ERROR: could not configure recon-all parameters Killed 2. ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0Or 3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the developer cannot be verified. mac OS cannot verify that this app is free from malware. I googled the third error message and tried "Allow anyways" from the privacy setting. Then the next message pops up, then the next and the next. Could you please help me to understand the cause of the above 3 error messages? I tried to redownload freesurfer as well as python but none worked. Thank you in advance. Best,Alice_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview crashes when trying to load volumes
by fsbuild 16 Jan '24

16 Jan '24

External Email - Use Caution  It would help for us to know what your machine is running, e.g., linux or MacOS (Intel or Silicon Mac) - and what the version is for the operating system, e.g. Linux Ubuntu 22, MacOS 12, etc.  If you are running Linux on Windows thru either WSL or a VM then please mention that and if the Windows host is running Win 10 or 11. - R. On Jan 12, 2024, at 11:52, Ford, Jamie K <j.ford(a)imperial.ac.uk> wrote:        External Email - Use Caution        Hello,Please could I get some advice on my installation? I've downloaded version 7.4.0 using the same steps described in the installation video MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=Attac… seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like on the video). Freeview then crashes. This is the same for any volume. Could someone please advice? Any guidance would be greatly appreciated.Many Thanks,Jamie_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Sample registration question
by Mirsol Choi 16 Jan '24

16 Jan '24

External Email - Use Caution Hi there Freesurfer, I am currently using freesurfer to take DTI metrics (FA, MD) from hippocampal subfields. At this point of my exploration with freesurfer, I am able to correctly register the hippocampal subfields and diffusion data, and obtain my FA values from the subfields. However, this is at the individual subject level. I will eventually need to register all of my samples in the same space for me to do a group analysis. However I am unsure what the order of registration should be for this process to be feasible. Does this order seem feasible for accurate analysis? 1) recon-all all of my subjects 2) dt_recon all of my subjects (one of the outputs is a registration file, which has registered the DTI data to outputs of recon-all) 3) run the hippocampus segmentation command on all subjects (segmentHA_T1.sh) to obtain hippocampal subfield segmentation 4) register the segmentation file to the FA maps (output of dt_recon) using vol2subfield command 5) After creating a subfield-FA map for each subject, spatial normalize the samples onto the same space using *mri_vol2vol* Thank you so much for taking the time reading my question. If there is a different method to spatially normalizing my datasets, or if there is a more optimal order of registration, I'd be happy to hear from you. Thank you, M

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