External Email - Use Caution
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, https://secure-web.cisco.com/1__PHy5riz1krqgipNavAJIc6annOjWAPD9Cy3snHRwj0xm... If freesurfer was previously installed with the linux package tools then it should work to uninstall it with,$ sudo apt remove freesurfer… answer y to all prompts ... If you unarchived the *.tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory. With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try, $ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb… wait for install to finish … $ cd$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ————Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjectsMNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview$ freeview… freeview should open an empty window … … quit freeview and try opening this example volume … $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz If you see the attached image, then freeview/Qt is essentially working. - R.
On Oct 14, 2023, at 14:14, Andrei Bieger <andreibieger@gmail.com> wrote: External Email - Use Caution Hi, all!I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer.When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.<Screenshot from 2023-10-14 15-06-44.png>I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case.Any help with that?-- Andrei Bieger_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
[image: Screenshot from 2023-10-15 11-58-02.png]
Em dom., 15 de out. de 2023 às 00:23, fsbuild fsbuild@contbay.com escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPD...
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with, $ sudo apt remove freesurfer … answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb … wait for install to finish …
$ cd $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ———— Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview $ freeview … freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger andreibieger@gmail.com wrote:
External Email - Use CautionHi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer. When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case. Any help with that? -- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5Rk...
How/when was your surface created? Can you send mris_info output of your pial surface? I’m wondering if it has volume geometry information.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Andrei Bieger Sent: Sunday, October 15, 2023 11:06 AM To: fsbuild fsbuild@contbay.com Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
[cid:image001.png@01DA0003.73152B40]
Em dom., 15 de out. de 2023 às 00:23, fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubun...https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPDNhGt713qUWGKL3EcQhDe8khRBY-nUPRwl-nZIMHUALIpOT4_EFjQl4LlfzRrOWfqziqqpbGFKxZZfvVS6E8t14OeXwRIzU40NLKf76swGwMc1jGxxZ7R9MtHrCFMFfHuJ8e7pF9EqWBSlZllSh-q_KNKsqUKa272keCfxL1RX4LPT3q14oK3F2tOTUTFlS28k6CKJlUBq6h23xdOOetk6Cz4-bZhpsBkkEl9ATlzTVrGV8LVPQtuT53Kfs7Vl266wbjQ6vih4dyDzsN03V/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with, $ sudo apt remove freesurfer … answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb … wait for install to finish …
$ cd $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ———— Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview $ freeview … freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger <andreibieger@gmail.commailto:andreibieger@gmail.com> wrote:
External Email - Use Caution
Hi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer. When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case. Any help with that? -- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5RkvcYYiGcJF01nDEBIrnpY3oqe5R9ReKMqufLOtskKgCr5hVDnFD9_HFYNZxLmJ02lpf-YMOhD4kzvRgaNhA2Cl9fQp5U9IEvDmmpBPRKDAGP8NGU3T210Fge5FWaL47oxXYCXdaph4-fpe9xgI6VWOi09oUffW9oKJ_BMxF7qNKZzRwNfMUjgWoxWkiekAGamFp2_u_jjtSrE2tNoYyuf7N3O3GkMFr52iTpjo_Yb7FQoJrXPtd3QsFoLuQlqSOPJu0pP9mNILTpeHd3KH-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
-- Andrei Bieger
External Email - Use Caution
The problem is, I'm having the same issue with the Bert sample that comes with the freesurfer download. I'm not able to mri_info the pial surfaces as the function seems to work only with volumes. When I use it with the brainmasks of my own project the work just fine. Also, all files are being displayed just fine at my university desktop. The problem is with my laptop, and I can't figure it out.
Best, Andrei
Em seg., 16 de out. de 2023 às 08:37, Huang, Yujing < YHUANG43@mgh.harvard.edu> escreveu:
How/when was your surface created? Can you send mris_info output of your pial surface? I’m wondering if it has volume geometry information.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Andrei Bieger *Sent:* Sunday, October 15, 2023 11:06 AM *To:* fsbuild fsbuild@contbay.com *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution *Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
Em dom., 15 de out. de 2023 às 00:23, fsbuild fsbuild@contbay.com escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1YaPL5xy1e3QtiP1ra0lfzsAsvWOZxmjszEoPXvLcaXma4v... https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPDNhGt713qUWGKL3EcQhDe8khRBY-nUPRwl-nZIMHUALIpOT4_EFjQl4LlfzRrOWfqziqqpbGFKxZZfvVS6E8t14OeXwRIzU40NLKf76swGwMc1jGxxZ7R9MtHrCFMFfHuJ8e7pF9EqWBSlZllSh-q_KNKsqUKa272keCfxL1RX4LPT3q14oK3F2tOTUTFlS28k6CKJlUBq6h23xdOOetk6Cz4-bZhpsBkkEl9ATlzTVrGV8LVPQtuT53Kfs7Vl266wbjQ6vih4dyDzsN03V/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with,
$ sudo apt remove freesurfer
… answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb
… wait for install to finish …
$ cd
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ————
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1
FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects
MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview
$ freeview
… freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger andreibieger@gmail.com wrote:
External Email - Use Caution *Hi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer.
When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case.
Any help with that?
--
Andrei Bieger
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/16jM5uI6nNdKgJnJeig_sJtNK4fNbdI1rCyuHZoHNvkI8bG... https://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5RkvcYYiGcJF01nDEBIrnpY3oqe5R9ReKMqufLOtskKgCr5hVDnFD9_HFYNZxLmJ02lpf-YMOhD4kzvRgaNhA2Cl9fQp5U9IEvDmmpBPRKDAGP8NGU3T210Fge5FWaL47oxXYCXdaph4-fpe9xgI6VWOi09oUffW9oKJ_BMxF7qNKZzRwNfMUjgWoxWkiekAGamFp2_u_jjtSrE2tNoYyuf7N3O3GkMFr52iTpjo_Yb7FQoJrXPtd3QsFoLuQlqSOPJu0pP9mNILTpeHd3KH-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
--
Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16jM5uI6nNdKgJnJeig_sJtNK4fNbdI1rCyuHZoHNvkI8bG... 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/1oR4SebEQvjfImFCdymGqZRS8RJQhnUBtDCFCQ-9NoNzR_C... < https://secure-web.cisco.com/1oR4SebEQvjfImFCdymGqZRS8RJQhnUBtDCFCQ-9NoNzR_C... .
mri_info is for volumes. mris_info works with surfaces.
Which version of Freesurfer are you using?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Andrei Bieger Sent: Monday, October 16, 2023 10:25 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution The problem is, I'm having the same issue with the Bert sample that comes with the freesurfer download. I'm not able to mri_info the pial surfaces as the function seems to work only with volumes. When I use it with the brainmasks of my own project the work just fine. Also, all files are being displayed just fine at my university desktop. The problem is with my laptop, and I can't figure it out.
Best, Andrei
Em seg., 16 de out. de 2023 às 08:37, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> escreveu: How/when was your surface created? Can you send mris_info output of your pial surface? I’m wondering if it has volume geometry information.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andrei Bieger Sent: Sunday, October 15, 2023 11:06 AM To: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
[cid:image001.png@01DA001C.1E93D4E0]
Em dom., 15 de out. de 2023 às 00:23, fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubun...https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPDNhGt713qUWGKL3EcQhDe8khRBY-nUPRwl-nZIMHUALIpOT4_EFjQl4LlfzRrOWfqziqqpbGFKxZZfvVS6E8t14OeXwRIzU40NLKf76swGwMc1jGxxZ7R9MtHrCFMFfHuJ8e7pF9EqWBSlZllSh-q_KNKsqUKa272keCfxL1RX4LPT3q14oK3F2tOTUTFlS28k6CKJlUBq6h23xdOOetk6Cz4-bZhpsBkkEl9ATlzTVrGV8LVPQtuT53Kfs7Vl266wbjQ6vih4dyDzsN03V/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with, $ sudo apt remove freesurfer … answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb … wait for install to finish …
$ cd $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ———— Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview $ freeview … freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger <andreibieger@gmail.commailto:andreibieger@gmail.com> wrote:
External Email - Use Caution
Hi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer. When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case. Any help with that? -- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5RkvcYYiGcJF01nDEBIrnpY3oqe5R9ReKMqufLOtskKgCr5hVDnFD9_HFYNZxLmJ02lpf-YMOhD4kzvRgaNhA2Cl9fQp5U9IEvDmmpBPRKDAGP8NGU3T210Fge5FWaL47oxXYCXdaph4-fpe9xgI6VWOi09oUffW9oKJ_BMxF7qNKZzRwNfMUjgWoxWkiekAGamFp2_u_jjtSrE2tNoYyuf7N3O3GkMFr52iTpjo_Yb7FQoJrXPtd3QsFoLuQlqSOPJu0pP9mNILTpeHd3KH-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
-- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/16jM5uI6nNdKgJnJeig_sJtNK4fNbdI1rCyuHZoHNvkI8bGhuvOjOKGXFoNr36JGNfceB1G9nnAhTymbNHfR8TC3gw9GoUBVIas2WT_b3kW31sdOFA789wetKrc7F9C5SrfeJJj0PV71eCyBaeAkn_cAQet-UvshjVPyQQM9aaxy2dBIl6TW77l5stvn_Q82Z8P4v-KNUQWjxUICT1XoNTVupzINbDCNfuNedXdKQY4fnsrhinHsfbLDVtFaKwxAEXEcwphZzmOcbXSLYu9Tz3cXZr04EjE5Pfs3UrVszwbzi2p1Bg2LZufhcMZ34_Hqi/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1oR4SebEQvjfImFCdymGqZRS8RJQhnUBtDCFCQ-9NoNzR_C3MW3mBLuuK45wMxOv5NzqEsKypQfTd-ZRQwhlnuNC4E20OHMPNCSCfyZY_pJLY1EQMr8rNFNPZwmtXfj1hoBU4qKX-Lre5CwPCzoho1TJVFzicRjeX7oqX6PkuQcL-Oj40vo0yfV61ljV6Oti9b6o8BgYUSaMg9wzvYCFmq9lh_qBycIZXlb6CVDmppIaJkLEeGElxQOFqjC1y2nLvENx24tJK0hI2rpkqYj2JH90APowKDlHkPvNNAxKyvh70tFR2bjYfDu9sNqjfRTRC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1oR4SebEQvjfImFCdymGqZRS8RJQhnUBtDCFCQ-9NoNzR_C3MW3mBLuuK45wMxOv5NzqEsKypQfTd-ZRQwhlnuNC4E20OHMPNCSCfyZY_pJLY1EQMr8rNFNPZwmtXfj1hoBU4qKX-Lre5CwPCzoho1TJVFzicRjeX7oqX6PkuQcL-Oj40vo0yfV61ljV6Oti9b6o8BgYUSaMg9wzvYCFmq9lh_qBycIZXlb6CVDmppIaJkLEeGElxQOFqjC1y2nLvENx24tJK0hI2rpkqYj2JH90APowKDlHkPvNNAxKyvh70tFR2bjYfDu9sNqjfRTRC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
-- Andrei Bieger
External Email - Use Caution
Nice! Here it goes for lh.pial. Also, it is freesurfer v7.4.1 (freesurfer_ubuntu22-7.4.1_amd64.deb https://secure-web.cisco.com/1r-pSD1Uu4XOpL1j1283yDyBECdR3MY-yLnamVWC7zbjI9MwmEPnTx5XTNx33ZNS3rJe7V4kGmvuAo0dcj8QOu8u6KMZmprx2r2fRc2CGI4jrbeqg8pu7hCAbSEExNH_1ztFoPjwTnqZraYzt7qTkomooGwrDC16fJvkmYRWcaP3CP2Inb7tNx4SutNfMbW7i0UZLw2GE2iSSXJt9wLp_pplOwq_Icds3GdlcJrSOWu-qjG5Vi8OCFDC6jZeFy4UBpzX9Di_ayI43HzDq4rlevthoF1FlSHXagTe2D6A5a7-Urhyi8Z-SbnkfagdULod5/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb) running on Ubuntu 22.04.3 installed on a fresh VirtualBox VM running on an HP Intel-I7 laptop, running Windows 11 Pro.
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 132602 num faces : 265200 num strips : 0 surface area: 108995 vg.valid: 1 AvgFaceArea 0.410993 AvgVtxArea 0.821973 AvgVtxDist 1.022856 StdVtxDist 0.442829 ctr : (-28.7116, -16.3092, 37.6244) original vertex space : surfaceRAS vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, -0.0000) c_(ras) : ( 5.6654, 26.6386, -17.9153) file : /mnt/A-NVME/mosaic-pd/neuroimagem/FS_OUTPUTS/100001_I1473172/mri/wm.mgz Volume Geometry vox2ras -1.00000 0.00000 0.00000 133.66544; 0.00000 0.00000 1.00000 -101.36142; 0.00000 -1.00000 -0.00000 110.08471; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: ProgramName: mris_remove_intersection ProgramArguments: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-23:36:58-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: andrei Machine: motox Platform: Linux PlatformVersion: 6.2.0-27-generic CompilerName: GCC CompilerVersion: 8.4.0 mris_info creationtime 2023/10/16-14:40:04-GMT sysname Linux hostname Ubuntu1 machine x86_64 surfacefile surf/lh.pial hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 132602 nfaces 265200 total_area 108995.218750 group_avg_vtxarea_loaded 0 avgfacearea 0.410993 avgvtxarea 0.821973 avgvtxdist 1.022856 stdvtxdist 0.442829 vtx0xyz -8.073509 -100.566986 17.722403 num_intersecting_faces 0
Em seg., 16 de out. de 2023 às 11:35, Huang, Yujing < YHUANG43@mgh.harvard.edu> escreveu:
mri_info is for volumes. mris_info works with surfaces.
Which version of Freesurfer are you using?
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Andrei Bieger *Sent:* Monday, October 16, 2023 10:25 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution *The problem is, I'm having the same issue with the Bert sample that comes with the freesurfer download.
I'm not able to mri_info the pial surfaces as the function seems to work only with volumes. When I use it with the brainmasks of my own project the work just fine.
Also, all files are being displayed just fine at my university desktop. The problem is with my laptop, and I can't figure it out.
Best,
Andrei
Em seg., 16 de out. de 2023 às 08:37, Huang, Yujing < YHUANG43@mgh.harvard.edu> escreveu:
How/when was your surface created? Can you send mris_info output of your pial surface? I’m wondering if it has volume geometry information.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Andrei Bieger *Sent:* Sunday, October 15, 2023 11:06 AM *To:* fsbuild fsbuild@contbay.com *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution *Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
Em dom., 15 de out. de 2023 às 00:23, fsbuild fsbuild@contbay.com escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Y7-xXwlygVwfmu2sKIICe6dZGFGV7aPw5hiNrcl9eg2jGF... https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPDNhGt713qUWGKL3EcQhDe8khRBY-nUPRwl-nZIMHUALIpOT4_EFjQl4LlfzRrOWfqziqqpbGFKxZZfvVS6E8t14OeXwRIzU40NLKf76swGwMc1jGxxZ7R9MtHrCFMFfHuJ8e7pF9EqWBSlZllSh-q_KNKsqUKa272keCfxL1RX4LPT3q14oK3F2tOTUTFlS28k6CKJlUBq6h23xdOOetk6Cz4-bZhpsBkkEl9ATlzTVrGV8LVPQtuT53Kfs7Vl266wbjQ6vih4dyDzsN03V/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with,
$ sudo apt remove freesurfer
… answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb
… wait for install to finish …
$ cd
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ————
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1
FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects
MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview
$ freeview
… freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger andreibieger@gmail.com wrote:
External Email - Use Caution *Hi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer.
When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case.
Any help with that?
--
Andrei Bieger
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wvjdmpJ7ZvYHWFoYlq8PnJFNNInDjA3eqrWUeGd8rRRmrE... https://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5RkvcYYiGcJF01nDEBIrnpY3oqe5R9ReKMqufLOtskKgCr5hVDnFD9_HFYNZxLmJ02lpf-YMOhD4kzvRgaNhA2Cl9fQp5U9IEvDmmpBPRKDAGP8NGU3T210Fge5FWaL47oxXYCXdaph4-fpe9xgI6VWOi09oUffW9oKJ_BMxF7qNKZzRwNfMUjgWoxWkiekAGamFp2_u_jjtSrE2tNoYyuf7N3O3GkMFr52iTpjo_Yb7FQoJrXPtd3QsFoLuQlqSOPJu0pP9mNILTpeHd3KH-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
--
Andrei Bieger
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wvjdmpJ7ZvYHWFoYlq8PnJFNNInDjA3eqrWUeGd8rRRmrE... https://secure-web.cisco.com/16jM5uI6nNdKgJnJeig_sJtNK4fNbdI1rCyuHZoHNvkI8bGhuvOjOKGXFoNr36JGNfceB1G9nnAhTymbNHfR8TC3gw9GoUBVIas2WT_b3kW31sdOFA789wetKrc7F9C5SrfeJJj0PV71eCyBaeAkn_cAQet-UvshjVPyQQM9aaxy2dBIl6TW77l5stvn_Q82Z8P4v-KNUQWjxUICT1XoNTVupzINbDCNfuNedXdKQY4fnsrhinHsfbLDVtFaKwxAEXEcwphZzmOcbXSLYu9Tz3cXZr04EjE5Pfs3UrVszwbzi2p1Bg2LZufhcMZ34_Hqi/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsI... https://secure-web.cisco.com/1oR4SebEQvjfImFCdymGqZRS8RJQhnUBtDCFCQ-9NoNzR_C3MW3mBLuuK45wMxOv5NzqEsKypQfTd-ZRQwhlnuNC4E20OHMPNCSCfyZY_pJLY1EQMr8rNFNPZwmtXfj1hoBU4qKX-Lre5CwPCzoho1TJVFzicRjeX7oqX6PkuQcL-Oj40vo0yfV61ljV6Oti9b6o8BgYUSaMg9wzvYCFmq9lh_qBycIZXlb6CVDmppIaJkLEeGElxQOFqjC1y2nLvENx24tJK0hI2rpkqYj2JH90APowKDlHkPvNNAxKyvh70tFR2bjYfDu9sNqjfRTRC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsI... https://secure-web.cisco.com/1oR4SebEQvjfImFCdymGqZRS8RJQhnUBtDCFCQ-9NoNzR_C3MW3mBLuuK45wMxOv5NzqEsKypQfTd-ZRQwhlnuNC4E20OHMPNCSCfyZY_pJLY1EQMr8rNFNPZwmtXfj1hoBU4qKX-Lre5CwPCzoho1TJVFzicRjeX7oqX6PkuQcL-Oj40vo0yfV61ljV6Oti9b6o8BgYUSaMg9wzvYCFmq9lh_qBycIZXlb6CVDmppIaJkLEeGElxQOFqjC1y2nLvENx24tJK0hI2rpkqYj2JH90APowKDlHkPvNNAxKyvh70tFR2bjYfDu9sNqjfRTRC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
--
Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1wvjdmpJ7ZvYHWFoYlq8PnJFNNInDjA3eqrWUeGd8rRRmrE... 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/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsI... < https://secure-web.cisco.com/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsI... .
Did you load everything from the command-line? Or did you load the surface first and then load the volume from the GUI.
Again, would be very helpful if you can send us the exact volume and surface files so we can diagnose.
On Oct 16, 2023, at 10:47 AM, Andrei Bieger <andreibieger@gmail.commailto:andreibieger@gmail.com> wrote:
External Email - Use Caution
Nice! Here it goes for lh.pial. Also, it is freesurfer v7.4.1 (freesurfer_ubuntu22-7.4.1_amd64.debhttps://secure-web.cisco.com/1r-pSD1Uu4XOpL1j1283yDyBECdR3MY-yLnamVWC7zbjI9MwmEPnTx5XTNx33ZNS3rJe7V4kGmvuAo0dcj8QOu8u6KMZmprx2r2fRc2CGI4jrbeqg8pu7hCAbSEExNH_1ztFoPjwTnqZraYzt7qTkomooGwrDC16fJvkmYRWcaP3CP2Inb7tNx4SutNfMbW7i0UZLw2GE2iSSXJt9wLp_pplOwq_Icds3GdlcJrSOWu-qjG5Vi8OCFDC6jZeFy4UBpzX9Di_ayI43HzDq4rlevthoF1FlSHXagTe2D6A5a7-Urhyi8Z-SbnkfagdULod5/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb) running on Ubuntu 22.04.3 installed on a fresh VirtualBox VM running on an HP Intel-I7 laptop, running Windows 11 Pro.
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 132602 num faces : 265200 num strips : 0 surface area: 108995 vg.valid: 1 AvgFaceArea 0.410993 AvgVtxArea 0.821973 AvgVtxDist 1.022856 StdVtxDist 0.442829 ctr : (-28.7116, -16.3092, 37.6244) original vertex space : surfaceRAS vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, -0.0000) c_(ras) : ( 5.6654, 26.6386, -17.9153) file : /mnt/A-NVME/mosaic-pd/neuroimagem/FS_OUTPUTS/100001_I1473172/mri/wm.mgz Volume Geometry vox2ras -1.00000 0.00000 0.00000 133.66544; 0.00000 0.00000 1.00000 -101.36142; 0.00000 -1.00000 -0.00000 110.08471; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: ProgramName: mris_remove_intersection ProgramArguments: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-23:36:58-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: andrei Machine: motox Platform: Linux PlatformVersion: 6.2.0-27-generic CompilerName: GCC CompilerVersion: 8.4.0 mris_info creationtime 2023/10/16-14:40:04-GMT sysname Linux hostname Ubuntu1 machine x86_64 surfacefile surf/lh.pial hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 132602 nfaces 265200 total_area 108995.218750 group_avg_vtxarea_loaded 0 avgfacearea 0.410993 avgvtxarea 0.821973 avgvtxdist 1.022856 stdvtxdist 0.442829 vtx0xyz -8.073509 -100.566986 17.722403 num_intersecting_faces 0
Em seg., 16 de out. de 2023 às 11:35, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> escreveu: mri_info is for volumes. mris_info works with surfaces.
Which version of Freesurfer are you using?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andrei Bieger Sent: Monday, October 16, 2023 10:25 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution The problem is, I'm having the same issue with the Bert sample that comes with the freesurfer download. I'm not able to mri_info the pial surfaces as the function seems to work only with volumes. When I use it with the brainmasks of my own project the work just fine. Also, all files are being displayed just fine at my university desktop. The problem is with my laptop, and I can't figure it out.
Best, Andrei
Em seg., 16 de out. de 2023 às 08:37, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> escreveu: How/when was your surface created? Can you send mris_info output of your pial surface? I’m wondering if it has volume geometry information.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andrei Bieger Sent: Sunday, October 15, 2023 11:06 AM To: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
<image001.png>
Em dom., 15 de out. de 2023 às 00:23, fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubun...https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPDNhGt713qUWGKL3EcQhDe8khRBY-nUPRwl-nZIMHUALIpOT4_EFjQl4LlfzRrOWfqziqqpbGFKxZZfvVS6E8t14OeXwRIzU40NLKf76swGwMc1jGxxZ7R9MtHrCFMFfHuJ8e7pF9EqWBSlZllSh-q_KNKsqUKa272keCfxL1RX4LPT3q14oK3F2tOTUTFlS28k6CKJlUBq6h23xdOOetk6Cz4-bZhpsBkkEl9ATlzTVrGV8LVPQtuT53Kfs7Vl266wbjQ6vih4dyDzsN03V/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with, $ sudo apt remove freesurfer … answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb … wait for install to finish …
$ cd $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ———— Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview $ freeview … freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger <andreibieger@gmail.commailto:andreibieger@gmail.com> wrote:
External Email - Use Caution
Hi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer. When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case. Any help with that? -- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5RkvcYYiGcJF01nDEBIrnpY3oqe5R9ReKMqufLOtskKgCr5hVDnFD9_HFYNZxLmJ02lpf-YMOhD4kzvRgaNhA2Cl9fQp5U9IEvDmmpBPRKDAGP8NGU3T210Fge5FWaL47oxXYCXdaph4-fpe9xgI6VWOi09oUffW9oKJ_BMxF7qNKZzRwNfMUjgWoxWkiekAGamFp2_u_jjtSrE2tNoYyuf7N3O3GkMFr52iTpjo_Yb7FQoJrXPtd3QsFoLuQlqSOPJu0pP9mNILTpeHd3KH-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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-- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1wvjdmpJ7ZvYHWFoYlq8PnJFNNInDjA3eqrWUeGd8rRRmrEc44VokI50KhXayYdZhvzRp4VR7fIyC-6Cg7ueRHt7SW1lXZfq7PvMZWNhF9bIf5iafhl0rpSkqXngSGScuU2yGHluxMDg3KtvVGoVbOIaL8dVBzpImLDVWwF8yJ4IjIAyXfivBXSgml8trC4Gm2-fUBk39yuIAa2ZP9X_BemxnPrx1LG8L5vVzvQvboreKuRh0UVnGGz9liqQGNqc24mH7TXPLcOlUX697A7E6e8KYQwlrEivajLfqIAUrE78zrbdRbEEBu6zFet59CS4w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsIYwf28kHJwQDXakEMefqmET0pnJLZvozGTaB4XPGQjpyWUOfU6LKEjYlm7wbwd55ORKEAvX7iC7ntpmyoG1WngDlHvgUJc4QqiifcEiwTrCEDg3RN2rf4TeILGRZO0bRfm1PlxhyqoqcgcX6HlqkT3GLyLOq2e0xvS8spECePb7FnjcUYZL9bQU8K0pN3RuEj8ZS_aOLvbHCzNivlq3oxwPYSgedh4XawjekD6af5t0j4Qkwf1kFKvqjEa6ivOvAkJoFKlWz-eaCwWotZ3c/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsIYwf28kHJwQDXakEMefqmET0pnJLZvozGTaB4XPGQjpyWUOfU6LKEjYlm7wbwd55ORKEAvX7iC7ntpmyoG1WngDlHvgUJc4QqiifcEiwTrCEDg3RN2rf4TeILGRZO0bRfm1PlxhyqoqcgcX6HlqkT3GLyLOq2e0xvS8spECePb7FnjcUYZL9bQU8K0pN3RuEj8ZS_aOLvbHCzNivlq3oxwPYSgedh4XawjekD6af5t0j4Qkwf1kFKvqjEa6ivOvAkJoFKlWz-eaCwWotZ3c/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
-- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I tried loading the files from the terminal and from freeview's GUI. They all return the same issue with the surfaces. And I just sent the files to your email.
Andrei
Em seg., 16 de out. de 2023 às 12:00, Wang, Ruopeng RWANG4@mgh.harvard.edu escreveu:
Did you load everything from the command-line? Or did you load the surface first and then load the volume from the GUI.
Again, would be very helpful if you can send us the exact volume and surface files so we can diagnose.
On Oct 16, 2023, at 10:47 AM, Andrei Bieger andreibieger@gmail.com wrote:
External Email - Use CautionNice! Here it goes for lh.pial. Also, it is freesurfer v7.4.1 (freesurfer_ubuntu22-7.4.1_amd64.deb https://secure-web.cisco.com/1r-pSD1Uu4XOpL1j1283yDyBECdR3MY-yLnamVWC7zbjI9MwmEPnTx5XTNx33ZNS3rJe7V4kGmvuAo0dcj8QOu8u6KMZmprx2r2fRc2CGI4jrbeqg8pu7hCAbSEExNH_1ztFoPjwTnqZraYzt7qTkomooGwrDC16fJvkmYRWcaP3CP2Inb7tNx4SutNfMbW7i0UZLw2GE2iSSXJt9wLp_pplOwq_Icds3GdlcJrSOWu-qjG5Vi8OCFDC6jZeFy4UBpzX9Di_ayI43HzDq4rlevthoF1FlSHXagTe2D6A5a7-Urhyi8Z-SbnkfagdULod5/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb) running on Ubuntu 22.04.3 installed on a fresh VirtualBox VM running on an HP Intel-I7 laptop, running Windows 11 Pro.
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 132602 num faces : 265200 num strips : 0 surface area: 108995 vg.valid: 1 AvgFaceArea 0.410993 AvgVtxArea 0.821973 AvgVtxDist 1.022856 StdVtxDist 0.442829 ctr : (-28.7116, -16.3092, 37.6244) original vertex space : surfaceRAS vertex locs : surfaceRAS Volume Geometry (vg) volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, -0.0000) c_(ras) : ( 5.6654, 26.6386, -17.9153) file : /mnt/A-NVME/mosaic-pd/neuroimagem/FS_OUTPUTS/100001_I1473172/mri/wm.mgz Volume Geometry vox2ras -1.00000 0.00000 0.00000 133.66544; 0.00000 0.00000 1.00000 -101.36142; 0.00000 -1.00000 -0.00000 110.08471; 0.00000 0.00000 0.00000 1.00000; Volume Geometry vox2ras-tkr -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; cmd[0]: ProgramName: mris_remove_intersection ProgramArguments: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: 7.4.1 TimeStamp: 2023/08/30-23:36:58-GMT BuildTime: Jun 14 2023 03:45:01 BuildStamp: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 User: andrei Machine: motox Platform: Linux PlatformVersion: 6.2.0-27-generic CompilerName: GCC CompilerVersion: 8.4.0 mris_info creationtime 2023/10/16-14:40:04-GMT sysname Linux hostname Ubuntu1 machine x86_64 surfacefile surf/lh.pial hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 132602 nfaces 265200 total_area 108995.218750 group_avg_vtxarea_loaded 0 avgfacearea 0.410993 avgvtxarea 0.821973 avgvtxdist 1.022856 stdvtxdist 0.442829 vtx0xyz -8.073509 -100.566986 17.722403 num_intersecting_faces 0
Em seg., 16 de out. de 2023 às 11:35, Huang, Yujing < YHUANG43@mgh.harvard.edu> escreveu:
mri_info is for volumes. mris_info works with surfaces.
Which version of Freesurfer are you using?
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Andrei Bieger *Sent:* Monday, October 16, 2023 10:25 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution *The problem is, I'm having the same issue with the Bert sample that comes with the freesurfer download.
I'm not able to mri_info the pial surfaces as the function seems to work only with volumes. When I use it with the brainmasks of my own project the work just fine.
Also, all files are being displayed just fine at my university desktop. The problem is with my laptop, and I can't figure it out.
Best,
Andrei
Em seg., 16 de out. de 2023 às 08:37, Huang, Yujing < YHUANG43@mgh.harvard.edu> escreveu:
How/when was your surface created? Can you send mris_info output of your pial surface? I’m wondering if it has volume geometry information.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Andrei Bieger *Sent:* Sunday, October 15, 2023 11:06 AM *To:* fsbuild fsbuild@contbay.com *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"
External Email - Use Caution *Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
<image001.png>
Em dom., 15 de out. de 2023 às 00:23, fsbuild fsbuild@contbay.com escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1VEryg9iOFr4lpPfW3NzpgHERyKLRvGSAZKpqNakFK-e7BI... https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPDNhGt713qUWGKL3EcQhDe8khRBY-nUPRwl-nZIMHUALIpOT4_EFjQl4LlfzRrOWfqziqqpbGFKxZZfvVS6E8t14OeXwRIzU40NLKf76swGwMc1jGxxZ7R9MtHrCFMFfHuJ8e7pF9EqWBSlZllSh-q_KNKsqUKa272keCfxL1RX4LPT3q14oK3F2tOTUTFlS28k6CKJlUBq6h23xdOOetk6Cz4-bZhpsBkkEl9ATlzTVrGV8LVPQtuT53Kfs7Vl266wbjQ6vih4dyDzsN03V/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with,
$ sudo apt remove freesurfer
… answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb
… wait for install to finish …
$ cd
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ————
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1
FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects
MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview
$ freeview
… freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger andreibieger@gmail.com wrote:
External Email - Use Caution *Hi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer.
When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case.
Any help with that?
--
Andrei Bieger
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1mSPbcF7cC6Xc7bijcMLreTx6OQVIEVwts-QNqIgZawCFcW... https://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5RkvcYYiGcJF01nDEBIrnpY3oqe5R9ReKMqufLOtskKgCr5hVDnFD9_HFYNZxLmJ02lpf-YMOhD4kzvRgaNhA2Cl9fQp5U9IEvDmmpBPRKDAGP8NGU3T210Fge5FWaL47oxXYCXdaph4-fpe9xgI6VWOi09oUffW9oKJ_BMxF7qNKZzRwNfMUjgWoxWkiekAGamFp2_u_jjtSrE2tNoYyuf7N3O3GkMFr52iTpjo_Yb7FQoJrXPtd3QsFoLuQlqSOPJu0pP9mNILTpeHd3KH-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Andrei Bieger
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--
Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1mSPbcF7cC6Xc7bijcMLreTx6OQVIEVwts-QNqIgZawCFcW... https://secure-web.cisco.com/1wvjdmpJ7ZvYHWFoYlq8PnJFNNInDjA3eqrWUeGd8rRRmrEc44VokI50KhXayYdZhvzRp4VR7fIyC-6Cg7ueRHt7SW1lXZfq7PvMZWNhF9bIf5iafhl0rpSkqXngSGScuU2yGHluxMDg3KtvVGoVbOIaL8dVBzpImLDVWwF8yJ4IjIAyXfivBXSgml8trC4Gm2-fUBk39yuIAa2ZP9X_BemxnPrx1LG8L5vVzvQvboreKuRh0UVnGGz9liqQGNqc24mH7TXPLcOlUX697A7E6e8KYQwlrEivajLfqIAUrE78zrbdRbEEBu6zFet59CS4w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dEJ-TX-1IWKSH0Av0iWyWXHblKC4Z_5ng4eBE1PGw1oyO5... https://secure-web.cisco.com/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsIYwf28kHJwQDXakEMefqmET0pnJLZvozGTaB4XPGQjpyWUOfU6LKEjYlm7wbwd55ORKEAvX7iC7ntpmyoG1WngDlHvgUJc4QqiifcEiwTrCEDg3RN2rf4TeILGRZO0bRfm1PlxhyqoqcgcX6HlqkT3GLyLOq2e0xvS8spECePb7FnjcUYZL9bQU8K0pN3RuEj8ZS_aOLvbHCzNivlq3oxwPYSgedh4XawjekD6af5t0j4Qkwf1kFKvqjEa6ivOvAkJoFKlWz-eaCwWotZ3c/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1dEJ-TX-1IWKSH0Av0iWyWXHblKC4Z_5ng4eBE1PGw1oyO5... https://secure-web.cisco.com/1h_94TaJOhJbljMHSopxknGSYunfGaWUq9qjpl7iUa4cwsIYwf28kHJwQDXakEMefqmET0pnJLZvozGTaB4XPGQjpyWUOfU6LKEjYlm7wbwd55ORKEAvX7iC7ntpmyoG1WngDlHvgUJc4QqiifcEiwTrCEDg3RN2rf4TeILGRZO0bRfm1PlxhyqoqcgcX6HlqkT3GLyLOq2e0xvS8spECePb7FnjcUYZL9bQU8K0pN3RuEj8ZS_aOLvbHCzNivlq3oxwPYSgedh4XawjekD6af5t0j4Qkwf1kFKvqjEa6ivOvAkJoFKlWz-eaCwWotZ3c/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
-- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1mSPbcF7cC6Xc7bijcMLreTx6OQVIEVwts-QNqIgZawCFcW...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1mSPbcF7cC6Xc7bijcMLreTx6OQVIEVwts-QNqIgZawCFcW... 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/1dEJ-TX-1IWKSH0Av0iWyWXHblKC4Z_5ng4eBE1PGw1oyO5... < https://secure-web.cisco.com/1dEJ-TX-1IWKSH0Av0iWyWXHblKC4Z_5ng4eBE1PGw1oyO5... .
Would it be possible to send us the volume and the surface files? If the volume geometric info from the surface is missing or wrong, it would be unlikely to align with the volume.
Ruopeng
On Oct 15, 2023, at 11:06 AM, Andrei Bieger <andreibieger@gmail.commailto:andreibieger@gmail.com> wrote:
External Email - Use Caution
Hello! Thank you for the reply.
I created a new VM with a fresh Ubuntu 22.04.3 install, got the OS up to date (apt update && upgrade), downloaded and installed the "freesurfer_ubuntu22-7.4.1_amd64.deb" via apt-get as you suggested and the bert/mri volume was displayed just fine on freeview. Yet when I add the subject`s pial surfaces using freeview`s GUI, the same problem happened. Please, see below.
<Screenshot from 2023-10-15 11-58-02.png>
Em dom., 15 de out. de 2023 às 00:23, fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> escreveu:
Freesurfer 7.4.1 on Ubuntu 20 uses its own versions of Qt libraries and not the system versions. So if your setup is looking for or finding system versions of those libraries, then freesurfer may be installed incorrectly and/or could be finding the wrong Qt libraries via use of environment variables like LD_LIBRRY_PATH or Qt*. (I would try not to set LD_LIBRARY_PATH and Qt environment variables in your shell environment before source’ing the freesurfer setup script).
I suggest you remove whatever freesurfer distribution you have on the machine and do a clean re-install of 7.4.1 using the .deb package installer which you can download via the link, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubun...https://secure-web.cisco.com/1kpuTk9_R5kskmqF_6o6rua0GGLqHxifzAoRK6cMSgrTpPDNhGt713qUWGKL3EcQhDe8khRBY-nUPRwl-nZIMHUALIpOT4_EFjQl4LlfzRrOWfqziqqpbGFKxZZfvVS6E8t14OeXwRIzU40NLKf76swGwMc1jGxxZ7R9MtHrCFMFfHuJ8e7pF9EqWBSlZllSh-q_KNKsqUKa272keCfxL1RX4LPT3q14oK3F2tOTUTFlS28k6CKJlUBq6h23xdOOetk6Cz4-bZhpsBkkEl9ATlzTVrGV8LVPQtuT53Kfs7Vl266wbjQ6vih4dyDzsN03V/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
If freesurfer was previously installed with the linux package tools then it should work to uninstall it with, $ sudo apt remove freesurfer … answer y to all prompts ...
If you unarchived the *..tag.gz file somewhere then “rm -rf” should work on the root freesurfer directory.
With the previous freesurfer installation removed, cd to where you downloaded the freesurfer_ubuntu20-7.4.1_amd64.deb and try,
$ sudo apt-get -y install ./freesurfer_ubuntu20-7-dev_amd64.deb … wait for install to finish …
$ cd $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 ———— Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni
$ which freeview /usr/local/freesurfer/7.4.1/bin/freeview $ freeview … freeview should open an empty window …
… quit freeview and try opening this example volume …
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
If you see the attached image, then freeview/Qt is essentially working.
- R.
On Oct 14, 2023, at 14:14, Andrei Bieger <andreibieger@gmail.commailto:andreibieger@gmail.com> wrote:
External Email - Use Caution
Hi, all!
I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer. When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)"
After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image.
<Screenshot from 2023-10-14 15-06-44.png>
I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case. Any help with that? -- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/10qa5i61mRFQjh_bcTHlgVXeRcNyHdVRN5wzqxX-Dbmh5RkvcYYiGcJF01nDEBIrnpY3oqe5R9ReKMqufLOtskKgCr5hVDnFD9_HFYNZxLmJ02lpf-YMOhD4kzvRgaNhA2Cl9fQp5U9IEvDmmpBPRKDAGP8NGU3T210Fge5FWaL47oxXYCXdaph4-fpe9xgI6VWOi09oUffW9oKJ_BMxF7qNKZzRwNfMUjgWoxWkiekAGamFp2_u_jjtSrE2tNoYyuf7N3O3GkMFr52iTpjo_Yb7FQoJrXPtd3QsFoLuQlqSOPJu0pP9mNILTpeHd3KH-/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
-- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Andrei Bieger -
fsbuild -
Huang, Yujing -
Wang, Ruopeng