Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30066 discussions

Re: [Freesurfer] Freeview 'quit unexpectedly' before opening
by fsbuild 10 Feb '23

10 Feb '23

External Email - Use Caution When you say you are running Mojave, I think you probably meant to write 10..14.6 (not 10.16.6). You could check you have the latest version of XQuartz (2.8.5) installed from,https://secure-web.cisco.com/11eALbuyxL0_txSil8AchFZPgix3GCpAuJbqcYDFJ… You may need to reboot the machine after installing Xquartz. Once back up, open a new terminal window and run the bash shell, $ bash Try putting your license file, e.g., license.txt. in your $HOME directory, and then set the environment variable FS_LICENSE to its absolute path, e.g. $ cd $HOME$ head -1 license.txtme(a)somewhere.org.  <—— email address you used to register with $ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEme(a)somewhere.org.  <—— email address you used to register with Then the usual setup,$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Then try opening an empty Freeview window again,$ freeview - R. On Feb 8, 2023, at 14:28, Rankin McGugin <rankin.mcgugin(a)gmail.com> wrote:<freeview_2023-02-08-122744_Rankins-MacBook-Pro.crash>

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Request for 7 zip password
by Nathaniel Bailey 09 Feb '23

09 Feb '23

External Email - Use Caution Hello, I would like the passcode for the 7 zip file FS_7_2_0_Ubuntu_18_04_06.ova.7z so that I can install the Freesurfer virtual image.

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change labels name
by John Anderson 09 Feb '23

09 Feb '23

External Email - Use Caution Dear Freesurfer, I have a volumetric atlas in nifti format. I can open this atlas in freeview. Using the Lookup Table>FreesurferColorLUT, I can see how every label has a specific color. When I move the mouse cursor over an area of this atlas. I can see the name of that region (label). My question is how can I edit the name of the regions in that atlas. I am sorry if my question is basic. I couldn't figure out how to do it :( Thanks for any advice you may provide. John

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Freeview 'quit unexpectedly' before opening
by Rankin McGugin 09 Feb '23

09 Feb '23

External Email - Use Caution Hello, I am a longtime FS user. I have read threads on this topic but no suggestions work in my case. I have the license file in place. I removed my previous version of FS and have updated to 7.3.2. However, now when I try to start Freeview, I get this problem report before the app even opens: [image: image.png] I have tried downloading the standalone Freeview, but get the same error. I have restarted the computer, completely removed everything and redownloaded it, but still the same issue persists. I am using macOS Mojave, 10.16.6 Are you able to guide me how to fix this and open Freeview? Thank you! *Rankin W. McGugin, PhD *Research Assistant Professor Department of Psychology Vanderbilt University email: rankin.mcgugin(a)vanderbilt.edu work phone: (615) 322-4644

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Directory
by Asa Borzabadi Farahani 08 Feb '23

08 Feb '23

External Email - Use Caution Hi there experts! I’m hoping to use the surfreg function on some data in which I can’t make any modifications to the subject directory (I’m using a cluster and the data is for public use thus prohibits any changes to it). I want to use the fsaverage_sym as my target file, though the function seems to only be looking for this folder within the subjects directory. Thus when running the following command: surfreg --s 126426 --t /project/60019995/coopapap/data/HCP/fsaverage_sym --lh I get the following error: ERROR: cannot find /project/60019995/coopapap/data/HCP/fsaverage_sym in /tmp/HCP I’m wondering if there is a workaround to using this command even when I can’t make any modifications to the subjects directory. To summarize, I’d like all outputs to go to a personal folder, and I’d like to use a template file that is in my personal folder. Thank you kindly. Asa Farahani

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MGH35 template
by Mark Wagshul 08 Feb '23

08 Feb '23

External Email - Use Caution Dear Freesurfer developers, Hi, this message may have slipped through the cracks, hope someone can help us out on this. We're looking for the T1 image that goes along with (i.e. in same space, or at least in same participants) as the MGH35_HCP_FA_template image which is used in TRACULA? Does such a template exist, and if so, would it be possible to share? Thanks so much! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Along- tract multiple comparison result visualisation and summary interpretation
by miracooloz 08 Feb '23

08 Feb '23

External Email - Use Caution Hello,I have questions regarding the along-tract stats using mri_glmfit and mri_glmfit-sim with permutation for version 7.2.1) I ran it and I found a significant result (see attached summary file) where I expected/found a negative association between FA and clinical score. how do I know the entire length of the tract and how much was affected based on the summary file; should I be interpreting the results from the summary file differently?2) Also when performing clusterwise correction for multiple comparison for along-tract analyses, should the bonferroni flag (--2spaces) be included? This is because it wasn't mentioned/included in the tracula statistics tutorial nor the publication "Using diffusion MRI data acquired with ultra-high gradient strength to improve tractography in routine-quality data". 3) Lastly, is it appropriate to embed the perm.th13.neg.sig.cluster.mgh from mri_glmfit-sim in dmri_trk2trk? Many thanks,PaulSent from my Galaxy

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[FreeSurfer] Help on installation of Freesurfer on Ubuntu 18 on Windows 11
by Krystal Xiwing Yau 08 Feb '23

08 Feb '23

External Email - Use Caution Dear FreeSurfer users, I tried to install the newest version of FreeSurfer 7.3.2 on ubuntu 18.04.6 VB Image. I have run the following commands before installing: $ sudo apt-get dist-upgrade $ sudo apt-get upgrade $ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'freesurfer' instead of './freesurfer_ubuntu18-7.3.2_amd64.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: freesurfer : Depends: xorg-dev but it is not going to be installed E: Unable to correct problems, you have held broken packages. I even installed apititude to try installing the package, but the error was still there: $ sudo aptitude install ./freesurfer_ubuntu18-7.3.2_amd64.deb Couldn't find any package whose name is ".", but there are 33955 packages which contain "." in their name: (too many to show, the limit is 40) Unable to apply some actions, aborting The previous version of 7.2.0 FreeSurfer was not imported successfully either. The appliance was 100% imported to the VB but there was none on the menu but another Ubuntu that I am trying to use. [cid:9ba00d21-b812-49da-8337-ce587d9f8dc5] Would someone kindly advise please? I am running Windows 11. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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password for 7z OVA file
by Andre Padua 07 Feb '23

07 Feb '23

External Email - Use Caution Hi everyone, I’d like to receive the password for the 7z ova file please. The file i have is FS_7_2_0_ubuntu_18_04_06.ova.7z. Thank you, Andre

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Fwd: mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 07 Feb '23

07 Feb '23

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