External Email - Use Caution I could be wrong, but maybe that error is a function of what code path is being executed, the order of operations to render the graphics, etc. It may not be as straightforward as either all images are going to work or none are going to work. I would try to test on a known/supported system. If you still get the same errors, then that would help us reproduce it on the systems we have. - R.
On Aug 8, 2023, at 22:42, DS <zky...@126.com> wrote: External Email - Use Caution Hi expert,Thanks for discussing it. I really appreciate it. That's very helpful. I have forwarded this message to admin, so that he will install it. But, I have another question. Before I visualize these images, I previously successfully loaded lh.white and lh.pial from another subject. If our system is not compatible with Freeview, why can I show these images from other subjects? Technically, under the current system, Freeview would not have worked with any images. Do you have any thoughts? Thank you so much.PS. I agree with your suggestions. We recently moved from RHEL 8 to RHEL 9, we have discarded RHEL 8. So, I guess that's why I met these issues.At 2023-08-09 10:21:46, "fsbuild" <fsbu...@contbay.com> wrote: External Email - Use Caution Thank you for posting that output. It shows you are running RHEL or Red Hat Enterprise Linux 9.1 (or the officially supported release downstream from CentOS9). That explains why your version of mesa packages is rev 22.So your best option is to try installing the 7.4.1 CentOS8 Stream installer, https://secure-web.cisco.com/142cnesLA-45N-BegLaDTx7pgSNN6br6URDohmLiZMSgsrfzEfa79RqfL6SnuLw9WoJjAeGGujPuT7JYf5mNNXTV-xOzV-DqHUDD5RCr3es5FGacccgKrIVuhc1WiFWx7ANXcGmvRYO59IDT1sZCsijD34nzoDxNwjGbVsAXQiwRs0h-vxi5g15fhef4fyMSExmhRpvKM_TKU5_txLv_PIr8-exZaAKHsfWBdWO9uwHUIPRjl1JUNxk7uBPVm-yaOKtrOpaFhFC0Vx1eXE8eT508hgn_00T0vzP_BDnLmXIMWwjMVBsljYJd2lyw7Ejjr4bQKnCNG53eeQ_phXccPlw/https%3A%2F%2Fsurfer.nmr.mgh..harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-CentOS8-7.4.1-1.x86_64.rpm, e.g., via,$ sudo yum install ./freesurfer-CentOS8-7.4.1-1.x86_64.rpmAfter a successful install, you would set FREESURFER_HOME to /usr/local/freesurfer/7.4.1-1 and then source the freesurfer setup script under that directory.While it may install just fine, there is no guarantee everything is going to work correctly with the newer versions of system libraries in RHEL 9. We have not tested on and currently do not officially support freesurfer running on RHEL 9/CentOS9 Stream.If you continue to have issues, you might want to inquire to your system administrators if a RHEL 8 or Ubuntu 22 machine is available to run freesurfer on. Barring that, you could create and run a VM (virtual machine) or container to host one of the linux OS’s we have installers for under that download link (https://secure-web.cisco.com/1X9AQaZtJeadUY-H3cja_TNqCr6QrBvjw4KkCn4svX1XWGAQsCKVat5kT1COo4pwScvia_GbE82kCt1RhcgGUIMk254SNsD4cMiA38OHfX-k_DbdCbbaFEGuLXsXEabyPuxOf1db61-SQNLc9mZu_Mx6I3v8429PuRxAj5BnP9P_PynV0m7S6T3q8ttWUkSjVKgo5wN27AOdGPjKQrWH8UQlmCcrAMp2wv9BH2O63MhWZA2An4p6a7H-a91TLc0lIb07JF-QTf88IKNR8Y_F-DHVISl9L4FnF3rgh9_6NKxS4DqaSPbalWMsjAY0jJcaRQLTgiYhhO-r259RjF73hTw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads). The supported OS's are CentOS 8, 7 and Ubuntu 22, 20, 18. You could host that VM or container on top of Red Hat Enterprise Linux 9.1 or most any other OS.RHEL has its own built in virtualization software called “qemu”. You system, administrators may already have qemu setup and working on your RHEL 9.1 machine. If so, you could ask them to setup qemu to run RHEL 8 and then install freesurfer-CentOS8-7.4.1-1.x86_64.rpm in that VM.Please note that it is easier to run Freeview in a VM compared to a container in order to view images.- R.On Aug 8, 2023, at 20:38, DS <zky...@126.com> wrote: External Email - Use Caution Hi expert,Thanks for your reply. I have contacted our admin to fix the installer issue, as our admin installed this FreeSurfer. But, at the same time, I try to get the version of our system by running "cat /etc/os-release", i.e.NAME="Red Hat Enterprise Linux"VERSION="9.1 (Plow)"ID="rhel"ID_LIKE="fedora"VERSION_ID="9.1"PLATFORM_ID="platform:el9"PRETTY_NAME="Red Hat Enterprise Linux 9.1 (Plow)"ANSI_COLOR="0;31"LOGO="fedora-logo-icon"CPE_NAME="cpe:/o:redhat:enterprise_linux:9::baseos"HOME_URL="https://secure-web.cisco.com/1ovUBbgYTLCz1nbzkl9474qBgKoMJVy6A6BR-gSZxobrLQ_R6we7_M4qCeJ0Jd3zyjMIOqgp3qbJuwlaCqRo7x_Tfbq4wveSynoRNHxir4YSSFQ65oU_yuVobT4Ge0oA-l-qJW0etVIzOXcn8b5hBFsNu1f2u2JH6ixjlLZzBFIRsRiUpAPkmdOOWjcDB1g2N20l3FnnaOZavct1pX0aI2bV-utnTAC4-YDAEoqXBD1tOUbAtraUOH6h4rPLKPq324zpus0qkI_hMhyr-2pKL2dzNPqapn24Uh4SVP4i3jd26lGotlPV663TvpI701mPDvQVmVhbS7yd6jGndRKDf_w/https%3A%2F%2Fwww.redhat.com%2F"DOCUMENTATION_URL="https://secure-web.cisco.com/1YHt_3Kl_WACiMrQZPigOxi-y-JpM1LXc_Y3FoRtkAm3yxIx6loFj9cBGeTSCZXKLoGc8d626OtrDqw9bLRvOkfMets-g_nXk78Bmz8l80qawCNYq2whf5GgMT7j1BvRc-3MbIPKJN1y1HXe-DLGzwghjYIB8lvOzj_KC5kcy-8wfpkvos-EwddFPnDrK0PEgSBS8C9ruEbcTlyrb-NwRRgmGA1ocdcCAuj8nUsijCmN7QOMlUkxMj1QlM9SVzyOsJv4Qz1IdGkGBbA4Q2YpimkJFtPFC6Uskn5oeBuSGNFEuHARepdHwMtiE6vXhB0z-E9dx5WtBVOa3EjzSfD2jPg/https%3A%2F%2Faccess.redhat.com%2Fdocumentation%2Fred_hat_enterprise_linux%2F9%2F"BUG_REPORT_URL="https://secure-web.cisco.com/15PdMKi4XHIUQ2p4okhnqW4F7Bc7TAi1USdeSlxfZ7p9h8WHnVpCCpibEy5AVXDya4KvavslTRr7ys7C_JnRjsiZNpWc0YSqURHQmS85YIQtALcl0tgYxEAD4YDZvqa7byLgP8LwGGHTg4kRKO5YgcUIIFvC9tJY7ctjd7wd-uZgU1AMUf03_mIKtwsXhlJzJjgNlyK53-1_VmvCAvSBZS5xy0euctv08GO3Od48uwzJUvzGuYLois0ft_Z0uYEOhnAybTakDFoiOluVeW7dfDzW6X0baV25txwtUr6OOqLOHSpvFyOIDgfSHYsAr3ubHPkJL4gtEX2QkTte3sItqWw/https%3A%2F%2Fbugzilla.redhat.com%2F"REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 9"REDHAT_BUGZILLA_PRODUCT_VERSION=9.1REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"REDHAT_SUPPORT_PRODUCT_VERSION="9.1"Once I have any updates, I will let you know. Thanks.At 2023-08-09 02:58:47, "fsbuild" <fsbu...@contbay.com> wrote: External Email - Use Caution The output in your previous email lists an error from a mesa version 22 header file found on your system under mesa-22.0.3/src/mesa/vbo. Mesa 22 implements the OpenGL 4.6 API which may not work reliably with some graphics card drivers.It might help to know what OS release you are running by sending along the output from,$ cat /etc/os-releaseYou could try setting a minimal environment and ensure LD_LIBRARY_PATH is not in use before setting up the freesurfer environment, e.g.,$ export PATH=/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin$ unset LD_LIBRARY_PATH.... then setup the freesurfer environment ...$ export FREESURFER_HOME=/your/path/to/freesurfer/install$ source $FREESURFER_HOME/SetUpFreeSurfer.shIf you have not already done so, I would also try downloading and running (with sudo) the freesurfer 7.4.1 .rpm or .deb file installer that matches your system via the links under, https://secure-web.cisco.com/19mV_2omzOOMClnHd5VkjlNUycKu9VqctfxoKta5Q498bJRWKoa_naL5uHQm7jZiPB3fc4vV8QE2Tx5WnzeopIAE5f8ZStSzANwJugc13OZUoKN5Td62omdZVKyW44p9_ER2SyKP1xl26v7kg2Z5eP_o6KeFRM0QfoVBPL0rlt9otzk5BljH4mtQJeAw6TNORMwam751361ICslgTd24WGt1aF3gYgSu0fsY19S4i3M-CtEmwJkNAnRK0RHBE48ULp0aO1dOssEoXqJ-V9K7XAFJQ-tZHW3lhEPoHEaZGtBIVM1j2KUe2qdGyddwwBiuFR-yjK-GHY_SjPDe4lJKkjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads.%26nbsp; The installer might find a conflict with what's installed on your system (and refuse to proceed), or alternately change/add versions of some packages including mesa. If the install succeeds, then the path to FREESURFER_HOME you can try will be /usr/local/freesurfer followed by ../7.4.1 or ./7.4..1-1 depending upon your linux system.- R.On 8/8/23 11:22, DS (zky...@126.com) wrote: External Email - Use Caution I tried to load one surface first, and there is no problem. But, after I load the second surface, the GUI was suddenly closed, and reported the same error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed.I thought this might be a RAM issue, but I tried to load larger surface files, and then they can be loaded smoothly. That's why I am confused about it. Do you have any thoughts? Thanks..At 2023-08-08 22:28:44, "Wang, Ruopeng" <rwa...@mgh.harvard.edu> wrote: External Email - Use Caution I don’t think this is the case since you can load 1 surface without problem. What if you load one surface from the command-line, then load the other one from the GUI?On Aug 8, 2023, at 9:45 AM, DS <zky...@126.com> wrote: External Email - Use Caution Hi expert,Thanks for your feedback. I am also using 7.4.1. I remember we previously had an issue with loading libGLU when we use 7.3.2. So, we installed 7.4.1 to fix this issue. And now I am using 7.4.1. Do you think there might be something with other parts of this tool?Thank you so much.At 2023-08-08 21:27:34, "Wang, Ruopeng" <rwa...@mgh.harvard.edu> wrote: External Email - Use Caution What version of freesurfer are you using? I tried with 7.4.1 and the latest dev build, both can load these 2 files together without problem.On Aug 7, 2023, at 8:11 PM, DS <zky...@126.com> wrote: External Email - Use Caution Hi expert,Thanks for your tips. Here is the output after typing "mris_info lh.white"SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACEnum vertices: 159999num faces : 319994num strips : 0surface area: 98524.6vg.valid: 1AvgFaceArea 0.307895AvgVtxArea 0.615783AvgVtxDist 0.858784StdVtxDist 0.223460ctr : (-34.5623, -3.52124, 27.1753)original vertex space : surfaceRASvertex locs : surfaceRASVolume Geometry (vg)volume geometry:extent : (384, 384, 384)voxel : ( 0.5000, 0.5000, 0.5000)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) : (-2.4468, 9.5993, -9..7705)file : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgzVolume Geometry vox2ras-0.50000 0.00000 0.00000 93.55320;-0.00000 -0.00000 0.50000 -86.40073; 0.00000 -0.50000 0.00000 86.22952; 0.00000 0.00000 0.00000 1.00000;Volume Geometry vox2ras-tkr-0.50000 0.00000 0.00000 96.00000; 0.00000 0.00000 0.50000 -96.00000; 0.00000 -0.50000 0.00000 96.00000; 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: 7.4.0 TimeStamp: 2023/07/26-08:06:34-GMT BuildTime: May 10 2023 00:12:43 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e User: zhisha Machine: linc1 Platform: Linux PlatformVersion: 3.10.0-1160.76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5mris_infocreationtime 2023/08/07-23:56:25-GMTsysname Linuxhostname reslnvhpc0281machine x86_64surfacefile lh.whitehemicode 0talairach_flag 0rescale 0.000000nvertices 159999nfaces 319994total_area 98524.593750group_avg_vtxarea_loaded 0avgfacearea 0.307895avgvtxarea 0..615783avgvtxdist 0.858784stdvtxdist 0.223460vtx0xyz -10.953291 -78.142456 0.268743num_intersecting_faces 255If I type "mris_info lh.pial", the output is SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACEnum vertices: 159999num faces : 319994num strips : 0surface area: 119400vg.valid: 1AvgFaceArea 0.373132AvgVtxArea 0.746256AvgVtxDist 0.975444StdVtxDist 0.419796ctr : (-34.8974, -3.52912, 26.0063)original vertex space : surfaceRASvertex locs : surfaceRASVolume Geometry (vg)volume geometry:extent : (384, 384, 384)voxel : ( 0.5000, 0.5000, 0.5000)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) : (-2.4468, 9.5993, -9..7705)file : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgzVolume Geometry vox2ras-0.50000 0.00000 0.00000 93.55320;-0.00000 -0.00000 0.50000 -86.40073; 0.00000 -0.50000 0.00000 86.22952; 0.00000 0.00000 0.00000 1.00000;Volume Geometry vox2ras-tkr-0.50000 0.00000 0.00000 96.00000; 0.00000 0.00000 0.50000 -96.00000; 0.00000 -0.50000 0.00000 96.00000; 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: 7.4.0 TimeStamp: 2023/07/26-08:06:34-GMT BuildTime: May 10 2023 00:12:43 BuildStamp: freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e User: zhisha Machine: linc1 Platform: Linux PlatformVersion: 3.10.0-1160..76.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5mris_infocreationtime 2023/08/08-00:01:31-GMTsysname Linuxhostname reslnvhpc0281machine x86_64surfacefile lh.pialhemicode 0talairach_flag 0rescale 0.000000nvertices 159999nfaces 319994total_area 119400.148438group_avg_vtxarea_loaded 0avgfacearea 0.373132avgvtxarea 0.746256avgvtxdist 0.975444stdvtxdist 0.419796vtx0xyz -10.917007 -79.515175 0.469994num_intersecting_faces 261But, I only load lh.white or lh.pial, freeview can show it. If I load both at the same time, it does not work. Anyway, I uploaded both files to google drive, here is the link (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1xbUwsICRfi1E7lDL9hEEwJW8TX1HxMHXZNTvO56oqg8C-XYrUVeNLgXyqdzOb5xRiXrdj6EKc7AYzP0lH-ZNgnaS6RhkutAIbSCwBISlcjF3pd2YIPsVbRMFwJj5d2a2m9aBVbP2uXtaJ26OnVAHqx2Qx_ObjcLxp2-d89XNrHCDftNDYVwE2StHZfhrvHyatlpwgH6tCG5J9EHu-CShrtm9Z8KFW1nJAovTzhNswczgiFyUx2M-1qVfoZN2fkXWqnLiXVKV929SIv400gJqAZW8GEgq-u7iJM3n1HiGHwTxh5W8E2G8ANnr7i1D-molcl5Rk1OLUKFNLvWWmoAfYQ/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1bTm4_IzzLlN-WeYgW2N6eFaQxA0m6scZ%3Fusp%3Dsharing%C2%A0). Hopefully, these images could more info to solve the problem. Thank you so much for your help.Best,CainAt 2023-08-08 04:44:41, "Fischl, Bruce R.,PHD" <bfis...@mgh.harvard.edu> wrote: External Email - Use Caution Hmm, can you try running mris_info lh.white mris_info lh.pial and see if those work? What if you just bring up the pial and not the white? Maybe you can put those files in a dropbox and one of us (Ruopeng?) can take a look? From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 4:00 PMTo: Freesurfer support list <freesur...@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface External Email - Use Caution Hi expert,I do not think it's related to RAM. When I try to load some images larger than the image that it fails to load, it also works. So, I guess it might be related to other issues. PS. the current free RAM is 6GB. Best,Cain At 2023-08-08 03:49:29, "Fischl, Bruce R.,PHD" <bfis...@mgh.harvard.edu> wrote: External Email - Use Caution Maybe you are at the edge of how much ram you have in that machine? How much free memory do you have? From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 3:48 PMTo: Freesurfer support list <freesur...@nmr.mgh..harvard.edu>Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface External Email - Use Caution Hi expert,Thanks for your reply. I used the following command line.freeview -f \lh.white:edgecolor=blue \lh.pial:edgecolor=red I also tried to load these images by clicking the icons on the interface of Freeview. But, both approaches do not work. The first image it loads just flashed, and then it's closed when it started to load the second image. But, I tried some images from another subject, then it works.Best,Cain At 2023-08-08 03:13:52, "Fischl, Bruce R.,PHD" <bfis...@mgh.harvard.edu> wrote: External Email - Use Caution What is your freeview command line/ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of DSSent: Monday, August 7, 2023 2:51 PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] Use freeview to visualize white and pial surface External Email - Use Caution I have a question about freeview. Recently, when I loaded lh.pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed. But, if I load lh.pial or lh.white separately, I found it’s working. I guess there might be inconsistent parameters between the two files, because when I check another subject, both files can be visualized very well. Do you have any thoughts about this issue? Thank you so much for any suggestions. PS. Previously I posted this question with the images that I use to troubleshoot the problem. But, I received an email saying that "this message need approval from moderator, because the files are larger than expected". However, I never receive any update/reply from the moderator so far. Best,Cain_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZtTzHVi07t3guHFWU4KEEb7iZ_TSNGKJmu8x_cRjulChFSp57eGIY9x_ZA6LEjTPEYstpUt2dQhYm01e-lk29wERLRdh_gWF5KzcxkvtB3pb-HcUWmiPudi_PT6TqcFVs9Kwo-ycJWTssSsa8yScrl_i_-gE9Imi5lHRVbaDKDQKOysqBiKTydBZz1gfpltbd_mlz-guycn1YCyKD52NviJywWaW8zqwb4E_lIfxIseSsJc4Y0PskNQYSy6ECyjoMazDb0Uiud8K-HSBDYYRsbWpzZ0_8bKifTumkRD-hm7sFWxUlH9eRL17CjfZP7vwbrcIFethSCT7C7s1VpVFKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1mqOnvMY04s6NDHJ3oU95i_lFUMHr2FQSIyY3RDzc4kfiV3dcg7A3T6Rj4ZwAKTyjbU4z6tvbjoRvfMtzPZ9ZFm5w6V8_WSfl8CM0ZCOBnEdFnZsinOL90MKigrFz-WnuNSdwvwri4VLERzvqTylK_r94_BPGIwmwRrFDOdh9Xx6toIPjOFVQux_rWi6ekvE_83n8uFY_s0XMXsl-OAETh-FjrEzsOEK5bHEBIKPQVGKxGvMW3Kwp_F8P0Tsp4d_YUOGP_PV-DtE6HN8qUf-b3hbTGtJAbsdghGrErnl9N3ekST8skB3M6sOwUWBnPoKlUkLZS4YQMNuotK5NyagJpA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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. _______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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