Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

Freeview Edit options restricted
by Carlos Alcocer 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, When I try to do recon-edit, it does not let me click on certain options ie. changin the brush size. It additionally doesnt let me exit out of or minimize it. I am running the most recent version of freesurfer (7.3.2) on linux (wsl). I reinstalled/updated freeview but this did not resolve the issue. I have attached screen shot below. You cant see cursor but if i were to hover over brush size for example, the cursor would be a light gray and not let mec change any of the options. [image: image.png] Thank you, Carlos

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password
by Tsai, Perry 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, I would like to get the password for unzipping FS_7_2_0_ubuntu_18_04_06.ova.7z, thank you. *********************EMAIL DISCLAIMER********************* This email and any files transmitted with it may be confidential and are intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient or the individual responsible for delivering the e-mail to the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. If you have received this e-mail in error, please delete it and notify the sender or contact Privacy Office 312.355.5650.

1 0

pass code for FS 7.2.0 archive
by lzagorch＠gmail.com 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, Could you please send me the pass code for extracting the archive of FS 7.2.0 (FS_7_2_0_Ubuntu_18_04_06.ova.7z)? Thanks, Lyubomir

1 0

ERROR: cannot find or read transforms/talairach.m3z
by Fraser Aitken 07 Mar '23

07 Mar '23

External Email - Use Caution Hi all I have upgraded to 7.3.2 and i seem to be having issues running recon all after unto recon1. Basically, auto recon completes but after I have checked the brain masks and go to run auto recon 2 and 3 i get the following error reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z error: No such file or directory error: transforms/talairach.m3z: could not open transformCommand exited with non-zero status 255 @#@FSTIME 2023:03:07:14:29:54 mri_ca_label N 10 e 15.23 S 0.25 U 14.96 P 99% M 498868 F 9 R 123462 W 0 c 42 w 348 I 1568 O 0 L 1.48 1.71 1.24 @#@FSLOADPOST 2023:03:07:14:30:10 mri_ca_label N 10 1.37 1.67 1.24 Linux bioeng342-pc 5.4.0-144-generic #161-Ubuntu SMP Fri Feb 3 14:49:04 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Freesurfer exited with ERRORS at Tue Mar 7 14:30:10 GMT 2023 This is the command I am using to run the skull strip reconAllCommand = sprintf('recon-all -i %s -subjid ''Freesurfer'' -autorecon1 -multistrip -cw256 -cm',T1File); and these are the other commands % run autorecon2 reconAllCommand = 'recon-all -subjid ''Freesurfer'' -autorecon2 -cm'; unixCommand = sprintf('%s\n%s',subjectDirCommand,reconAllCommand); unix(unixCommand); % run autorecon3 reconAllCommand = 'recon-all -subjid ''Freesurfer'' -autorecon3 -cm'; unixCommand = sprintf('%s\n%s',subjectDirCommand,reconAllCommand); unix(unixCommand); % copy Freesurfer output to rootDir sourceDir = fullfile(Freesurfer,'Freesurfer'); targetDir = fullfile(rootDir,'Subject_data',subjects{iSubj}); unixCommand = sprintf('cp -r %s %s',sourceDir,targetDir); unix(unixCommand); Greatful for any suggestions of a fix

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VirtualBox pass code
by Jennifer Kilmer 07 Mar '23

07 Mar '23

External Email - Use Caution Hello, Is it possible to have the virtual box passcode sent to me? Thank you in advance! Jennifer

1 1

MRI image quality metrics
by MANSON ERIC NAAB 06 Mar '23

06 Mar '23

External Email - Use Caution Dear FreeSurfer experts, Please, I need your assistance and guidance on calculating the contrast-to-noise ratio (CNR) and signal-to-noise-ratio (SNR) of White matter, Gray matter, and CSF of the brain after recon-all. Thank you

5 7

mri_robust_register --minsize
by Proulx, Jean Sebastien 06 Mar '23

06 Mar '23

Hello, I am trying to register a full volume to a single slice, and I follow example 3 of mri_robust_register's help. I get the following error: Input image is smaller than min dimension: 1 < 16 Input dimensions (after conformalizing) MOV: 64 64 64 Input dimensions (after conformalizing) DST: 64 64 1 Specify larger minimum ... This error stays after adding --minsize 1 or --minsize, despite mri_robust_register recognizing the flag, as suggested by this terminal output: --minsize: Smallest dimension > 0 . Registration ran ok when replacing the single-slice with a 40-slice volume. Any idea on what is going on here? Thanks a lot for the good work and Have a good day! Sebastien

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Visualizing transparent surface with non transparent annotations
by Leonardo Tozzi 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Experts, I would like to use Freeview to achieve the following. I would like to visualize a transparent brain surface, with only some annotations visible. In other words, I would like the surface to be transparent, but the annotations I choose to visualize to not be transparent. Is there a way to achieve this? Thank you, Leonardo Tozzi, MD, PhD Director of Computational Neuroscience & Neuroimaging Program Stanford Center for Precision Mental Health and Wellness Stanford University ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 Connect with us! [signature_1075933358]<https://secure-web.cisco.com/10OmKEEhtSQzpfvnfJVDeLBEHHi9OqaBVJ9LAvZsQvsNWt…> [signature_1282923475] <http://secure-web.cisco.com/1I3hXNj6irLn6oQYZFgxz73In-4_EGzX-NMOPCnUJP3yv02…> [signature_911042299] <https://secure-web.cisco.com/10-8-bEWGWgfQnDhesaI2ZU2QywWqHHyTXTPc8TI7RfrgI…>

2 1

Re: [Freesurfer] Mac OS 13 Ventura
by fsbuild 06 Mar '23

06 Mar '23

External Email - Use Caution Hello Elmira, You can try downloading an installing the 7.3.2 package file, freesurfer-darwin-macOS-7.3.2.pkg, from https://secure-web.cisco.com/19NKhoH2W5uSEES-6x2_z8s-Qx5RJB0qwAFyHKCorvYwKi… Once downloaded, right-clicking on the package file and then selecting open should work.  There should also be a link to setup instructions on that page. - R. On 3/6/23 10:41, Elmira Hassanzadeh (elmitt(a)gmail.com) wrote:         External Email - Use Caution         Hi everyone, Could someone please direct me to the workaround instructions on installing Freesurfer on Mac M1 ultra on OS 13.0 Ventura? Thank you,Elmira _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1zSwVL2DeoKToXwAT4D4C9uxaS2pmJaYLtLmu4lG8MhZTN… 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://secure-web.cisco.com/1GDd7p1A6AR5iRMjhtYjllNXrg_98JDGa0HS424tO6n1Pr… <https://secure-web.cisco.com/1KQsyVOY-H0bVeMnNv1GKX_2WfslJnmFqbrvM1nSvqzHZ26pGC-7wtfjj_oFyeyd6EOcKzzyw2j5MuM_0Is3SC2iOXFJRLXPeShQvA2lDk50bVoZ1VsEIy8Mg6Zjy7CRx0WBxpPgL1F7FK8Bkv2xp7dieYZcUQmH_WgLH4jlur0Di011ddDKa80eFIdPt-6cATmzYD1iDuOD5pdevpdpFqk6f_9bH1omfJ6Izf3JRL59dY_BPXLOcpe0TlTIuc-GOxVB0a5xcxMuXb06MGJTX7DRmY682xG3NAhMFSuBew8Mclo6_oo9ytRR28MkYNCNTMeeQv_AQBcEy8rD0_jBozg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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.

1 0

Segment the centrum semiovale
by Julie Ottoy 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer team, I was wondering if FS has a way to segment the centrum semiovale? The freesurfer colorLUT table mentions "Centrum semiovale is also labled with 5001 (left) and 5002 (right)." (see https://secure-web.cisco.com/16ntnqYurxLXfYvZCsM5evs9fxRFquoTnxIkD0H4vCmJ3w… ) What does the "also" refer to in this description? Do the following rois represent the centrum semiovale ? : 5001 Left-UnsegmentedWhiteMatter 20 30 40 0 5002 Right-UnsegmentedWhiteMatter 20 30 40 0 Thank you for your help!

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Freesurfer March 2023