Freesurfer

freesurfer@nmr.mgh.harvard.edu

24 participants
30076 discussions

How to create white.deformed file in longitudinal pipeline
by 정범석 31 May '22

31 May '22

External Email - Use Caution Dear Freesurfer experts, I'm running GenericfMRIVolumeProcessingPipeline of HCP pipeline in longitudinal dataset(T1w and fMRI). After running longitudinal pipeline in freesurfer, I'd like to run script like below. bbregister --s ses-01 --mov Scout_gdc_undistorted2T1w_init.nii.gz --surf white.deformed --init-reg ./mri/transforms/eye.dat --bold --reg ./rfMRI_REST1_PA_fmap/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/EPItoT1w.dat --6 --o ./rfMRI_REST1_PA_fmap/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/Scout_gdc_undistorted2T1w.nii.gz However, "white.deformed" file in surf directory is not found in .long directory but in cross-section one. When I use "white.deformed" file in cross-section directory, an error message was occurred "  ERROR: number of vertices in ./surf/lh.thickness does not match surface (132608,133203)" How to create white.deformed file, appropriately, in the line of the longitudinal pipeline? Bumseok

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Request for password for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Arjun Singh 31 May '22

31 May '22

External Email - Use Caution Hello, Please provide me with the password for the virtual machine file for freesurfer (FS_7_2_0_Ubuntu_18_04_06.ova.7z) Thank you Regards, Arjun Singh

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pw for fs vm edition
by Niels Foit 31 May '22

31 May '22

External Email - Use Caution Hi guys, i require the unzip pw for fs vm on windows. Best niels

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Freesurfer passowrd
by nairulislam＠tutamail.com 31 May '22

31 May '22

External Email - Use Caution Hi there, I just downloaded the Freesurfer zip file that is meant to be used with the virtual box. I need the password of that zip file.

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Virtual Box Password
by Wojciech Górecki 31 May '22

31 May '22

External Email - Use Caution Hello I wanted to ask whether you can send me the pass code for VB image: FS_7_2_0_ubuntu_18_04_06.ova.7z Regards W. Górecki

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password request to expand archive (ubuntu)
by mariangela asimina 30 May '22

30 May '22

External Email - Use Caution Hello, I am writing to request a password for the zip file for the 7.2.0 release in Ubuntu, in order to install FreeSurfer on windows through the VirtualBox. Thank you in advance Mariangela Asimina

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Re: [Freesurfer] Pass code virtual box
by fsbuild 29 May '22

29 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 27, 2022, at 14:33, Max Hinrichs <hinrichs-max(a)web.de> wrote:        External Email - Use Caution        Hi,  I downloaded the FreeSurfer virtual box (https://secure-web.cisco.com/10EIfghQmCyH4hbcuz3ZyZ_H2_2dnkYSuUFkHCdmUoW5pi…) and wanted to ask whether you can send me the pass code. Best wishes, Max _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Using Freesurfer package in MLOps framework
by fsbuild 29 May '22

29 May '22

External Email - Use Caution Hello, The package and associated dependency tools that are part of an existing Linux OS use either the freesurfer .rpm (Redhat, CentOS, etc.. linux derivatives) or the .deb package file (Ubuntu, Debian, etc. linux derivatives) to dynamically determine what (if any) dependent packages need to be installed on the target linux system based upon the dependencies in the freesurfer package file.  Those dependencies are derived from the symbol versions compiled into the freesurfer binaries.  The point of using the .rpm or .deb installer files with the native linux system yum, rpm, dpkg, apt, etc. tools is so no one has to manually figure out the freesurfer dependencies - which could be different on any given linux system.   If you don’t have root/sudo privileges to install the .rpm or .deb files on a linux system, then you can unarchive the .tar.gz file (which provides no dependency checking).   You can see all the available packages for the current 7.2.0 release at https://secure-web.cisco.com/1uYwfyUWWoTgl9ozxMEZNw1QqBdCnOmN1uHLFI… - R. On May 29, 2022, at 03:57, 우앙청심환 <dlagudduf13(a)gmail.com> wrote:        External Email - Use Caution        Hi, I'm using a program based on the MLOps framework and just want to use the Freesurfer package in this. but I found the only installable file on the document page.so what I would like to ask is, is it possible to install and use the freesurfer package separately in an environment such as Google Colap, in addition to the existing method of extracting and installing freesurfer on Linux.. If possible, I wonder what is the dependency of the freesurfer package..Best regards.  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Using Freesurfer package in MLOps framework
by 우앙청심환 29 May '22

29 May '22

External Email - Use Caution Hi, I'm using a program based on the MLOps framework and just want to use the Freesurfer package in this. but I found the only installable file on the document page. so what I would like to ask is, is it possible to install and use the freesurfer package separately in an environment such as Google Colap, in addition to the existing method of extracting and installing freesurfer on Linux. If possible, I wonder what is the dependency of the freesurfer package. Best regards.

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Re: [Freesurfer] Unable to install Matlab runtime to run the SegmentHA function in Mac OS 12.4
by fsbuild 28 May '22

28 May '22

External Email - Use Caution Try running the install with sudo, e.g., $ sudo fs_install_mcr  R2014b If that does not work, you could try turning off the gatekeeper on MacOS (although this weakens your system security), and then see if the install works. $ sudo spctl --master-disable … then to re-enable the gatekeeper, $ sudo spctl --master-enable On May 26, 2022, at 23:18, Isabella Leung <I.Leung(a)westernsydney.edu.au> wrote:<Terminal screenshot.jpg>

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