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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/10GLtxtMlgiuFybMD0cY_brZC5MXIy0CPYlNkhR4pAp0qWa--GhQJiHj8Qg2Cnxw6n4YGGLiOnqs2cuLvIezt8pjUGyKCetqUKKb3EGLgoWpU4B9AAqOMoGNTxsN2fGuREkpfaspGdRCtbKD-h-jCpWhT0LfPXETsZYMvs947dBHn70uKim8t9Gaq0Ivttj02SzpOQx_5nqvKFI17sz_kHo2CzwdsP6N1NmiJSGx1Y9xlvIzT2YmBSU5Mn3GVIhyYzdEnX30k1nylBhrMM5oy79BbpEwlSBQW67rVWjoSsNGxVhqj2UQ4ukiXweKu8dRtAhehI-PIz8QUjiZNZjyDsA/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:
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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:
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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/1ISmWHEli28NnENV_byotaYOAH92Vv6ZabBjx2THy7qNhr5EzMQMhe-xRJLRCsgymSFe6hZgjJdPkTQRLVDf7ZKGlarE9Umknm7G80SY-qN0PV4x9e3gD03RqUzGN8GVU_eE9II-MJOZyJC5FKkXGW3-4mF-RrDpnwMeRM_1Np4QOdTHkUlbSqvWZ06cIkAEpW66NpohMZeXy3L9abgA1B1IPsqZeQuzm2A7rpouNT8Qevt9mllXZRUL3ZK9ZWFDVI1Qh2AuLNaGBuHWYBidPCh_o8nACLdJ6iCFhbsNqmI__Ek6KRHC8JLe99FkbVz8o3-NfNAvXrHUlcPV_qw_fWg/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,
Cain
At 2023-08-08 04:44:41, "Fischl, Bruce R.,PHD" <bfis...@mgh.harvard.edu>
wrote:
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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 <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface
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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:
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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 <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Use freeview to visualize white and pial surface
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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:
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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
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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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