Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] FreeSurfer VirtualBox Image
by fsbuild 06 Apr '22

06 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 5, 2022, at 21:56, Marc <mddirisi(a)lakeheadu.ca> wrote:        External Email - Use Caution        Hi there!I was following the FreeSurfer VirtualBox installation tutorial on the wiki (https://secure-web.cisco.com/1_udjFHwPLIJrynuPi7juHksX6N9r5hAnQtEydx919pNax…) and was wondering if I could get the password for the encrypted archive.Thanks in advance! _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Mri Convert Brucker MGRE files dicom to nii error
by Mateo Jean 06 Apr '22

06 Apr '22

External Email - Use Caution Hello FreeSurfer Developers I need to convert 512 dicom files from Bruker into .nii . I firstly add .dcm to my Bruker multi gradient echo phase files then enter the following command : mri_convert MRIm001.dcm phaseMGE.nii Here is the first message : reading from MRIm001.dcm... Starting DICOMRead2() dcmfile = /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm dcmdir = /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2 ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm break /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930 Ref Series No = 4 Found 514 files, checking for dicoms ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm break /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930 ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 Then 508 error messages like the three last lines appear. It ends with : First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 8 nslices = 63 ndcmfiles = 508 ERROR: the number of frames * number of slices does not equal the number of dicom files. I did a test with only 448 files (I just copy-paste the first 448 files = 7 TE * 64 slices) and I obtained the same error messages but the nifti files are created and seem usable (quick test with Fiji). Here are the last lines : First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting IsDWI = 1, IsPhilipsDWI = 0 Counting frames nframes = 7 nslices = 64 ndcmfiles = 448 INFO: rescale not needed PE Dir = COL (dicom read) Loading pixel data TR=50.00, TE=3.10, TI=0.00, flip angle=15.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to phaseMGR.nii... Saving bvals and bvecs I'm pretty new with mri convert and I don't understand why it stops converting to nii with 512 files (8 TE) but not 448 files for Brucker files. Best Regards, Mateo Version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

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FreeSurfer VirtualBox Image
by Marc 05 Apr '22

05 Apr '22

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MCRv84 issue on Freesurfer 7.2.0 on MacOS Monterey 12.2
by Ashwati Vipin (Dr) 05 Apr '22

05 Apr '22

External Email - Use Caution Dear Freesurfer Developers, I have recently downloaded Freesurfer 7.2.0 and am trying to run the hippocampal segmentation. I tried installing the Matlab 2014b compiler but when I run the command: sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr 2014b it repeatedly gives me the error: ./install: line 334: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.6Gemf2Ah/bin/unknown/install_unix: No such file or directory ls: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.6Gemf2Ah/install-target/v*: No such file or directory Following this I am unable to run the hippocampal subfield segmentation. Additionally, I also tried downloading the compiler separately and copying the bin/maci64 folder into a new directory under the freesurfer root directory labelled “MCRv84”. When I do this, it starts running for a second but then gives me the following error: Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64:/Applications/freesurfer/7.2.0/MCRv84//bin/maci64:/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64:/Applications/freesurfer/7.2.0/lib/gcc/lib: dyld[85643]: Library not loaded: @rpath/libmwmclmcrrt.8.4.dylib Referenced from: /Applications/freesurfer/7.2.0/MCRv84/bin/maci64/libmwlaunchermain.dylib Reason: tried: './libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//runtime/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//bin/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84//sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/lib/gcc/lib/libmwmclmcrrt.8.4.dylib' (no such file), '/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/MCRv84/bin/maci64/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/./libmwmclmcrrt.8.4.dylib' (no such file), '/Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/../../sys/os/maci64/libmwmclmcrrt.8.4.dylib' (no such file), '/usr/local/lib/libmwmclmcrrt.8.4.dylib' (no such file), '/usr/lib/libmwmclmcrrt.8.4.dylib' (no such file) /Applications/freesurfer/7.2.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 85643 Abort trap: 6 /Applications/freesurfer/7.2.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML BIOC_0001_v01_T1_FS /Users/ashwativipin/Desktop/Freesurfer/Stats/ 0.333333333333333333333333333333333333 /Applications/freesurfer/7.2.0/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.2.0/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.2.0/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.2.0/bin/fs_run_from_mcr /Applications/freesurfer/7.2.0/bin/' 0 Darwin Ashwatis-MacBook-Pro.local 21.3.0 Darwin Kernel Version 21.3.0: Wed Jan 5 21:37:58 PST 2022; root:xnu-8019.80.24~20/RELEASE_ARM64_T8101 arm64 T1 hippocampal subfields exited with ERRORS at Mon Apr 4 12:11:15 +08 2022 For more details, see the log file /Users/ashwativipin/Desktop/Freesurfer/Stats//BIOC_0001_v01_T1_FS/scripts/hippocampal-subfields-T1.log I have also attached the log file for you. Could you please help? I’m not sure what I’m doing wrong since the above steps worked just fine a few months ago. I also have matlab 2022 installed and am wondering if that could be interfering with this? Thanks so much! Hope to hear from you soon. Best, Ashwati ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

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Re: [Freesurfer] VM pass code request
by fsbuild 05 Apr '22

05 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 5, 2022, at 18:34, Nathan Bolander <nathan.bolander(a)gmail.com> wrote:        External Email - Use Caution        I am sending email to the list to request the pass code to extract the VM archive, as instructed in the Wiki. Best regards,Nathan _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer 7.2.0 release in Ubuntu 18d // .ova.7z password
by fsbuild 05 Apr '22

05 Apr '22

External Email - Use Caution Sending the info to your private email shortly. - R On Apr 5, 2022, at 07:44, ΑΙΚΑΤΕΡΙΝΗ ΝΑΛΕΝΤΖΗ-ΜΑΡΙΑΝΟΥ <biomed_rad20010(a)uniwa.gr> wrote:        External Email - Use Caution        Greetings team Freesurfer,Following the instructions in your wiki page, I’m sending you to kindly provide me with the .7z password for the said file (Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z).Thanks a lot in advance,Katerina Nalentzi _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VM pass code request
by Nathan Bolander 05 Apr '22

05 Apr '22

External Email - Use Caution I am sending email to the list to request the pass code to extract the VM archive, as instructed in the Wiki. Best regards, Nathan

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Still seeking Beta Testers for new FreeSurfer discussion platform
by Sennott, Liam Ricker 05 Apr '22

05 Apr '22

Hello again, FreeSurfer community, I’m reaching out to you again today because we are still in search of people who are willing to test our new FreeSurfer help platform. Thank you to those who have already responded; we will be reaching out to you shortly. The FreeSurfer administrative team is working on transitioning the current FreeSurfer mailing list infrastructure to a new, more user-friendly platform called Discourse. We’re still finalizing the website, so we’re looking for potential beta testers for this new platform. As a beta tester, you will post your questions to Discourse and interact with the FreeSurfer staff in discussion board format. Please email lsennott(a)mgh.harvard.edu<mailto:lsennott@mgh.harvard.edu> if you are interested in helping us test this new system! Thank you, Liam Sennott FreeSurfer Admin

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Freesurfer 7.2.0 release in Ubuntu 18d // .ova.7z password
by ΑΙΚΑΤΕΡΙΝΗ ΝΑΛΕΝΤΖΗ-ΜΑΡΙΑΝΟΥ 05 Apr '22

05 Apr '22

External Email - Use Caution Greetings team Freesurfer, Following the instructions in your wiki page, I’m sending you to kindly provide me with the .7z password for the said file (Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z). Thanks a lot in advance, Katerina Nalentzi

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Re: [Freesurfer] freeview crashes
by fsbuild 04 Apr '22

04 Apr '22

External Email - Use Caution Hello Stephen, I'll assume the VM is setup according to the online instructions, e.g., the VM is assigned 8G of RAM and 2 cores from the host machine.  I'll also assume you are opening files with freeview from within the VM's virtual disk, e.g., from the home directory you login to on the VM. I would try upgrading to the latest version of VirtualBox for Windows which is currently 6.1.32.  When you launch VirtualBox it should notify you there is a new version available and ask if you want to upgrade. Do you have some version of the Windows Subsystem for Linux (WSL) also installed?   That can sometimes be an issue, but the error you report does not look to be from that.. - R. "Ogier, Stephen E. (Assoc)" (stephen.ogier(a)nist.gov) April 4, 2022 at 13:41         External Email - Use Caution         Hi,   I’m new to Freesurfer, and I’m running into a reoccurring crash issue when I use freeview. I’m following the instructions at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1DlH8w4XzRPlr6j2W2uoSddaowTh89VvPAV2BtYs1gUDJd… After I open freeview, if I use the mouse to manipulate the image, eventually the program crashes and I receive this error message.   The instruction at 0x00007ffa0d9b3460 referenced memory at 0x0000000000000010. The memory could not be read.   Click on OK to terminate the program   I’ve received this kind of error multiple times. The addresses for the instruction varies, and the memory address has also been 0x0000000000000000.   Has anyone else come across this problem? For reference, I’m running the FS_7_2_0_ubuntu_18_04_06 VM in VirtualBox 6.1 on a Windows 10 PC (Version 20H2, OS Build 19042.1586).   Thanks,   Stephen Ogier, PhD Postdoctoral Associate, Magnetic Imaging Group, Applied Physics Division National Institute of Standards and Technology     _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/16a7qmMIdxOIWkXtmYujOCnPYSPLLLAva0RpyWvV3ipyeE… 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/1oxusVVqDl94uN0mIyLg01OrJsCHvrU4mMrkzcwa3yQrKE… <https://secure-web.cisco.com/1Sc1llL2poCCCGw_IR0ycNNKzwpiSjSMk6KIu2Xbq8_zn7FhTCJ5r2F2PPXirUE47fD-yf2NaguwUq6EMiBxC3nJWE4YQWAEJbhwTC8d4h7KmcEXa5ystUgaFZoFgspgdzxjsh6zIWK6C-U_H0zsjhJ8zxcAt_oyJoMQga1oNFpgOAA4idJSlhJlZpE0-glZqGrrSTxanNzC65g6pzvvAmPbzis_surNQw0AVJyJQW71tkXCo97viIry-nNNui2U-MBHIFa6kq3bNufd_uV56EQBIb2PSfmB5Io_o53-Zlsvv9AGH8SvscmjA-GM2ixWT/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.

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