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 <rwa...@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 <andreibie...@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.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 <
> yhuan...@mgh.harvard.edu> escreveu:
>
>> mri_info is for volumes. mris_info works with surfaces.
>>
>>
>>
>> Which version of Freesurfer are you using?
>>
>>
>>
>> Yujing
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@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 <
>> yhuan...@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-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Andrei Bieger
>> *Sent:* Sunday, October 15, 2023 11:06 AM
>> *To:* fsbuild <fsbu...@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 <fsbu...@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-e7BIcaZ08-LesKN0RgT00TOLLBjcLOs9rnx6I-8cFq4hVCj09F29DSaagFwAjAs0Ooqq2kgCT4UqQt-LuYCGjPzm4vWgjuAfD2xnUcTO9eepE9Jr5kqZAj2loS58zSAjFDgECk6rd2QVXeS-oqXRYf5oExsFpeJLNwtQ0Kk9o6u2py1A8ihgMEvRJepCIoMn2X8T2_I1FCBuxnh3REsqEiwuOvgfZAVPQhnlyxvXyhBNoz2vIaYviFVNniYCH5iORpZoJ-yj3mpH613qsCwcss/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu20-7.4.1_amd64.deb
>> <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 <andreibie...@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
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>>
>>
>>
>>
>>
>> --
>>
>> Andrei Bieger
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
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>> .
>>
>>
>>
>> --
>>
>> Andrei Bieger
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1dEJ-TX-1IWKSH0Av0iWyWXHblKC4Z_5ng4eBE1PGw1oyO5hBx2XCTZNUv7QK3Ak_SQi_ytBVsbIK4aGXvzJQBR_Jh_SlgRQgmtYV75VFc9vfHoNWpzz0ksZEeYUENHKJSvdZ5WOYO0wTOJ_U0unSs7IBUtwuwnvp7mz1PWmL0jsZ-HumAb77-gpBMPRHrmRkxQAp5b18R8jfHoe7lHke3hNtP1dhs0Ef4WQptQsqjFVCakUXJOK4pbwR4JImhfDUzpaCTJLOvnbCvhlw2VzU1XxGqpI9V0jqfYOIhJNz8Z7_61344kjZXSLL8JU72J4M/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <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_5ng4eBE1PGw1oyO5hBx2XCTZNUv7QK3Ak_SQi_ytBVsbIK4aGXvzJQBR_Jh_SlgRQgmtYV75VFc9vfHoNWpzz0ksZEeYUENHKJSvdZ5WOYO0wTOJ_U0unSs7IBUtwuwnvp7mz1PWmL0jsZ-HumAb77-gpBMPRHrmRkxQAp5b18R8jfHoe7lHke3hNtP1dhs0Ef4WQptQsqjFVCakUXJOK4pbwR4JImhfDUzpaCTJLOvnbCvhlw2VzU1XxGqpI9V0jqfYOIhJNz8Z7_61344kjZXSLL8JU72J4M/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <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-QNqIgZawCFcWanH08yshfe6b4ajwJuY2XBn7fPMwqM4Fif8LgoDKq6tzw5g4gcgj-KczcrH_11qQ885HaHUAM9D_zkgJ5_ChNhHPGkomMSWHc96S01Hf4wn6hXEbWfGwewkFbnD4e9Pc2yr6xAP3B3rw-YM_maJbKD3PuIr3rLGL9qIJ9RC1uMHAwgjPyAb_ZCfdNiwJ-Q43IW4oYeK9Wsr9dSWB6BuEylW6N1gt3XMgDelXlb4hlXSfx9BNGWa_RMT9FUQO1-nlcO9NvtVr5Df-tl37FE/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
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> https://secure-web.cisco.com/1mSPbcF7cC6Xc7bijcMLreTx6OQVIEVwts-QNqIgZawCFcWanH08yshfe6b4ajwJuY2XBn7fPMwqM4Fif8LgoDKq6tzw5g4gcgj-KczcrH_11qQ885HaHUAM9D_zkgJ5_ChNhHPGkomMSWHc96S01Hf4wn6hXEbWfGwewkFbnD4e9Pc2yr6xAP3B3rw-YM_maJbKD3PuIr3rLGL9qIJ9RC1uMHAwgjPyAb_ZCfdNiwJ-Q43IW4oYeK9Wsr9dSWB6BuEylW6N1gt3XMgDelXlb4hlXSfx9BNGWa_RMT9FUQO1-nlcO9NvtVr5Df-tl37FE/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
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> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1dEJ-TX-1IWKSH0Av0iWyWXHblKC4Z_5ng4eBE1PGw1oyO5hBx2XCTZNUv7QK3Ak_SQi_ytBVsbIK4aGXvzJQBR_Jh_SlgRQgmtYV75VFc9vfHoNWpzz0ksZEeYUENHKJSvdZ5WOYO0wTOJ_U0unSs7IBUtwuwnvp7mz1PWmL0jsZ-HumAb77-gpBMPRHrmRkxQAp5b18R8jfHoe7lHke3hNtP1dhs0Ef4WQptQsqjFVCakUXJOK4pbwR4JImhfDUzpaCTJLOvnbCvhlw2VzU1XxGqpI9V0jqfYOIhJNz8Z7_61344kjZXSLL8JU72J4M/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1dEJ-TX-1IWKSH0Av0iWyWXHblKC4Z_5ng4eBE1PGw1oyO5hBx2XCTZNUv7QK3Ak_SQi_ytBVsbIK4aGXvzJQBR_Jh_SlgRQgmtYV75VFc9vfHoNWpzz0ksZEeYUENHKJSvdZ5WOYO0wTOJ_U0unSs7IBUtwuwnvp7mz1PWmL0jsZ-HumAb77-gpBMPRHrmRkxQAp5b18R8jfHoe7lHke3hNtP1dhs0Ef4WQptQsqjFVCakUXJOK4pbwR4JImhfDUzpaCTJLOvnbCvhlw2VzU1XxGqpI9V0jqfYOIhJNz8Z7_61344kjZXSLL8JU72J4M/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


-- 
Andrei Bieger
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