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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/1zgttfpOv9tXml1yn3znDqspoPFHI3WZPqEBm_3S11YkrDgxHivmooBYvMw6ln_dxGOqJqXtAZVq5YYJaJ1NeZbiQ2RrFs0V5T3nyPht_hOMUbBe093VkwW0SG6Ot03_SJP3DF3294NvtEybN-15CxwRtTGbHYB5tXODb_2105A-l6wJUPAbWkYpInXNJxffT-eBXI71UVIi4a3-Eth8HI7v7qsLruXG0FuXCz92bZT-NQnnwiLkd1CwAXbJ3PuihF5gpCkkywpgZmJXitsnpItkdeOAgE52GHzuCi2Q2sTNZH3gaBnZTbOmaVTGH4DQe2CdDdoW3Wqj9so_lcgT5CQ/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.rpm
After 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/1pulYmk-u7kDvBllrG2bRmOYpOIoXRA-ubPcxbDKIWnQqUb_z4tAQ367GeRd4ZEs_xZhi6QXDMynjvBVuXmaMqgLhkCGv8jdgTAKYHzA1dPFc8MU9h4yCcFGcTVey-HcANCIGoJ5guh0fofsy6CNdFnf9VNOFGOeaoKjFrYlOk3dZghhJuqDuVw5eKEiuqqGzSHkGMh_ssHSiTJuRnqnoo5GwzsyKrj34kWV6IzvUVF3KZX341zYfmHLg-AVbQpiGRhLknAyqoGkCeLvEd9OlLrrDNgfhcLxYXU1Z0bxJhTeTS-iHHd-j_o6nFgr-2JQio9cwqTq2zlftYStnKylp7A/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/1f6Y6hUWd7xDBCl9LnVpK8l53wI3C4LWLCVGgl1g3Uz3WVdlWs_8NzF3kWmusLUYm0IBcP92cxNCl7PR5WULOzOD5fPcl1HaW92OT9AfyJ8u2ToVYAArNogVX_lysqXY-2gU_rifFhWX9dxpVyONEuY0AVPVd81nmIkcO_-ICsMwn0UfE_tAmy45oP3J2zxq9_5Oy_S0v28r5pvWRBDsLjNajepVL_CWdTZXgd0sNoEWkxZ0z6rVc5HwpmI48CA8ob9BGuNp3Iu78b6xzY0OAkXZa-ZqZzWfk6z5jXghQ9i2bni43Kax_JSlUhW1s41zKRyiKISQ5cdR3x9z_nTFhpg/https%3A%2F%2Fwww.redhat.com%2F";
DOCUMENTATION_URL="https://secure-web.cisco.com/1AjXEWchX4q5bbTSgrNlS1PUO67ul_eFejET1xRtRRg2urjzdMBxvIZ3faZLkrrjKHFskVgYLNWRagKRTYTOtoz9znpuxhIO-PHGl9rG1jkoVF-Unxe3ClJygAMlnYDf7i3Zos7jrfppgkZDgUQCkMdea4zRk9_03FzCRCUAtj_eao7dyMz40KclKOJRXO0qSAunDmgAhlVKrDMdIqzX1_c_3Sy1GQ-yeFcyI0KVy2dA-ygI876HArr3cjNGOWDpBe2JWB4UMRE62ci4Hi6WYINszr4xuJqQEwScWWSvl8D7vhsZ0_ApWCtfVuRTiWAdUTe09c3hnOIz0ZhezfDQD-A/https%3A%2F%2Faccess.redhat.com%2Fdocumentation%2Fred_hat_enterprise_linux%2F9%2F";
BUG_REPORT_URL="https://secure-web.cisco.com/1m2qSfvU2-AekZTLQZQaooIFVftxnS-EZk1G0PYEZ7r3EEjZIdn4R6hQRuUUrojWAtvZDZZy69slQOcNgKA3vFjvUCthW4cdwuXSdBRP6aPVDplwWqsUsP8XITS7bamF9PVN01y9yGJYY8_k_0RefB5mj2mASUbfIZjbR8APH7Q5WM-rDE5Ne7bwvZA1epwD9VseEAtOcLjKYRqd_r2UPA6P4vZfyyCRafgZ95ECqDNShBjaTdp9fNI2QpAi_Kkso7LiqOZj5kd87mT-Qejv2VAvhOZYzZMGer4wjIaK8mIqpWedUMzbO6JCNQ-RAk3lU0GAxgM2HAXQbJ-g8GurqKw/https%3A%2F%2Fbugzilla.redhat.com%2F";
REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 9"
REDHAT_BUGZILLA_PRODUCT_VERSION=9.1
REDHAT_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:
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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-release
You 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.sh
If 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/1pulYmk-u7kDvBllrG2bRmOYpOIoXRA-ubPcxbDKIWnQqUb_z4tAQ367GeRd4ZEs_xZhi6QXDMynjvBVuXmaMqgLhkCGv8jdgTAKYHzA1dPFc8MU9h4yCcFGcTVey-HcANCIGoJ5guh0fofsy6CNdFnf9VNOFGOeaoKjFrYlOk3dZghhJuqDuVw5eKEiuqqGzSHkGMh_ssHSiTJuRnqnoo5GwzsyKrj34kWV6IzvUVF3KZX341zYfmHLg-AVbQpiGRhLknAyqoGkCeLvEd9OlLrrDNgfhcLxYXU1Z0bxJhTeTS-iHHd-j_o6nFgr-2JQio9cwqTq2zlftYStnKylp7A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
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:
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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:
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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:
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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:
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Hi expert,
Thanks for your tips. Here is the output after typing "mris_info lh.white"
SURFACE INFO ========================================
type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 159999
num faces : 319994
num strips : 0
surface area: 98524.6
vg.valid: 1
AvgFaceArea 0.307895
AvgVtxArea 0.615783
AvgVtxDist 0.858784
StdVtxDist 0.223460
ctr : (-34.5623, -3.52124, 27.1753)
original vertex space : surfaceRAS
vertex locs : surfaceRAS
Volume 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.mgz
Volume 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: 4.8.5
mris_info
creationtime 2023/08/07-23:56:25-GMT
sysname Linux
hostname reslnvhpc0281
machine x86_64
surfacefile lh.white
hemicode 0
talairach_flag 0
rescale 0.000000
nvertices 159999
nfaces 319994
total_area 98524.593750
group_avg_vtxarea_loaded 0
avgfacearea 0.307895
avgvtxarea 0.615783
avgvtxdist 0.858784
stdvtxdist 0.223460
vtx0xyz -10.953291 -78.142456 0.268743
num_intersecting_faces 255
If I type "mris_info lh.pial", the output is
SURFACE INFO ========================================
type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 159999
num faces : 319994
num strips : 0
surface area: 119400
vg.valid: 1
AvgFaceArea 0.373132
AvgVtxArea 0.746256
AvgVtxDist 0.975444
StdVtxDist 0.419796
ctr : (-34.8974, -3.52912, 26.0063)
original vertex space : surfaceRAS
vertex locs : surfaceRAS
Volume 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.mgz
Volume 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: 4.8.5
mris_info
creationtime 2023/08/08-00:01:31-GMT
sysname Linux
hostname reslnvhpc0281
machine x86_64
surfacefile lh.pial
hemicode 0
talairach_flag 0
rescale 0.000000
nvertices 159999
nfaces 319994
total_area 119400.148438
group_avg_vtxarea_loaded 0
avgfacearea 0.373132
avgvtxarea 0.746256
avgvtxdist 0.975444
stdvtxdist 0.419796
vtx0xyz -10.917007 -79.515175 0.469994
num_intersecting_faces 261
But, 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/14qViTBOjJ5zpk4m2Ub0PJQ3rMKmLasMcHF0YU1AdHxppedTQNc8eIhwuonSG7XmsozZAzwVRwKGpTVqyDzyvhyyS1D_X6z2qeIpB1j7KgKy5l0LNQeAUP34wQECAqAp2ep0Wp98WjI-vCr5hhwgltUiP0zuvQifH6-e_qp5bOwlEhi7dMSrFmNnF5ZszBnxtsZbPqib1uZwHwm9Pwb1jwPuGgR3mYeCKqV2yOqB8CzLpXvW4ev75tFmUb9WyB6Bk1PwWS4Khzn1hHaLbyzHGcbj4945v9dVZsAn6YcsgzUSNHyQGFSZaEq3AUo3p5Oy9odcyaLj-uDMSnFmb6JkETA/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1bTm4_IzzLlN-WeYgW2N6eFaQxA0m6scZ%3Fusp%3Dsharing
). Hopefully, these images could more info to solve the problem. Thank you so
much for your help.
Best,
Cain
At 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 DS
Sent: Monday, August 7, 2023 4:00 PM
To: 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 DS
Sent: Monday, August 7, 2023 3:48 PM
To: 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 DS
Sent: Monday, August 7, 2023 2:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [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
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