Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Recon-all Note Completing
by Ledesma, Jason 07 Apr '20

07 Apr '20

External Email - Use Caution Hi, I am receiving an error when performing recon-all. See attached for recon-all log. Thanks. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)lundquist.org ___________________________________________________________________________________ LUNDQUIST Institute Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ___________________________________________________________________________________

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whether freesurfer version 7 still support GPU
by Frank Robert 07 Apr '20

07 Apr '20

External Email - Use Caution Hello Freesurfer team I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)." https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not. Thanks Frank

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hippocampus subfield segmentation using Siemen and GE scans
by Kate Marvel 07 Apr '20

07 Apr '20

External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different FOV? Thanks, Kate

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Chorid-plexus in Freesurfer reconall
by Lijun An 07 Apr '20

07 Apr '20

External Email - Use Caution Dear Freesurfer experts, I have a little question about the structure 'chorid-plexus', I am not very deep in brain anatomy and function. Could anyone have a sense of what is the normal range of this structure volume from Freesurfer reconall? I found that mean of 'chorid-plexus' in ADNI is around 1500 mm^3, when I ran reconall for my local subejcts (a local dataset), I found the mean of 'chorid-plexus' is around 800 mm^3. Could anyone give an explanation or a paper I could refer to for this 'chorid-plexus' structure? Thanks so much! Best Regards, An Lijun

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Permutation with Non-Orthogonal Matrices
by Hua, Jessica 06 Apr '20

06 Apr '20

External Email - Use Caution Hi FreeSurfer Experts, As recommended I ran the following command: mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces And I got the following error message: ERROR: Flag --perm-resid unrecognized. Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Re: [Freesurfer] Install Freesurfer on Ubuntu
by fsbuild 06 Apr '20

06 Apr '20

External Email - Use Caution Hello Stephan, There is some information here about packages to install in order to run freesurfer - see highlighted "apt-get install" commands. https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements I think you will also need to install these packages, libjpeg62_6b2-3_amd64.deb https://drive.google.com/file/d/1Zdd-C3EQEEww180OzxEk1WV0h9obZYkD/view?usp=… libpng12-0_1.2.54-1ubuntu1_amd64.deb https://drive.google.com/file/d/1OWQSWL8a3Y8f1Weiauj9Lr2d3mtvZOm5/view?usp=… We also have an Ubuntu VM you can download.  While you may prefer to run on your own Ubuntu machine, it could also serve as a reference for you to see what we installed on Ubuntu 18.04 (including those extra packages). https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - R. On Apr 6, 2020, at 16:50, Stephan <stephan.wunderlich22(a)gmail.com> wrote:        External Email - Use Caution        Hi,ist there an official guideline how to install Freesurfer on Ubuntu?Best,Stephan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Install Freesurfer on Ubuntu
by Stephan 06 Apr '20

06 Apr '20

External Email - Use Caution Hi, ist there an official guideline how to install Freesurfer on Ubuntu? Best, Stephan

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vertex number to MNI coordinates
by Marina Fernández 06 Apr '20

06 Apr '20

External Email - Use Caution Dear Freesurfer experts, I hope you can help me with the following questions: 1. What is the best way to know the MNI coordinates to which a vertex of a surface corresponds? 2. I have projected the surfaces of the subjects onto the average subject from this dataset. Can I know the MNI coordinates corresponding to a vertex of the average subject of my dataset? Or do I need to project it onto the fsaverage to know the correspondence to de MNI space? 3. I know that the average surface is constructed by computing the MNI305 coordinate at each vertex, But how can I obtain the MNI152 coordinates (instead of MNI305) to which a vertex corresponds? (if it is possible). Thank you very much in advance. Best regards, Marina

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Re: [Freesurfer] Ubuntu image asking for user credentials on startup
by fsbuild 06 Apr '20

06 Apr '20

External Email - Use Caution Hello Vi, I will send the password to your email. - R. On Apr 6, 2020, at 13:22, rudolfrentier <1q2s3c4f5t6h7m8k9o0o(a)gmx.net> wrote:      External Email - Use Caution        Hi!I wanted to try out FreeSurfer and followed the install guide fromhttps://surfer.nmr..mgh.harvard.edu/fswiki/VM_67_win with the linkedUbuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded2020-04-06 1:29 AM CEST).However, upon startup of the virtual machine, the Ubuntu installationasks me for my user credentials with a preselected "developer" user (seescreenshot attached). According to the install guide, the virtualmachine should just boot up to Desktop without requiring a password.Is there a default password I am supposed to use (I tried leaving thepassword field blank, "freesurfer", "FreeSurfer", "developer" but noneof those worked)?Thanks,Vi<FreeSurfer login prompt 2020-04-06 191708.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu image asking for user credentials on startup
by rudolfrentier 06 Apr '20

06 Apr '20

External Email - Use Caution Hi! I wanted to try out FreeSurfer and followed the install guide from https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67_win with the linked Ubuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-04-06 1:29 AM CEST). However, upon startup of the virtual machine, the Ubuntu installation asks me for my user credentials with a preselected "developer" user (see screenshot attached). According to the install guide, the virtual machine should just boot up to Desktop without requiring a password. Is there a default password I am supposed to use (I tried leaving the password field blank, "freesurfer", "FreeSurfer", "developer" but none of those worked)? Thanks, Vi

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