Re: [Freesurfer] Use freeview to visualize white and pial surface

8 Aug 2023


      External Email - Use Caution
&nbsp;
The output in your previous email lists an error from a mesa version 22 header file found on your system under&nbsp;mesa-22.0.3/src/mesa/vbo.&nbsp; 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)&nbsp; 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...; 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.&nbsp; 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 (zkypis@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.&nbsp;
.../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv:
 Assertion `used_next &lt;= 
save-&gt;vertex_store-&gt;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" &lt;RWANG4@mgh.harvard.edu&gt; 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 &lt;zkypis@126.com&gt; 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&nbsp;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" &lt;RWANG4@mgh.harvard.edu&gt; 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 &lt;zkypis@126.com&gt; wrote:
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Hi expert,
Thanks for your tips. Here is the output after typing "mris_info lh.white"
SURFACE INFO ========================================&nbsp;
type&nbsp; &nbsp; &nbsp; &nbsp; : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 159999
num faces&nbsp; &nbsp;: 319994
num strips&nbsp; : 0
surface area: 98524.6
vg.valid: 1
AvgFaceArea&nbsp; &nbsp; &nbsp; 0.307895
AvgVtxArea&nbsp; &nbsp; &nbsp; &nbsp;0.615783
AvgVtxDist&nbsp; &nbsp; &nbsp; &nbsp;0.858784
StdVtxDist&nbsp; &nbsp; &nbsp; &nbsp;0.223460
ctr&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: (-34.5623, -3.52124, 27.1753)
original vertex space&nbsp; &nbsp;: surfaceRAS
vertex locs&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: surfaceRAS
Volume Geometry (vg)
volume geometry:
extent&nbsp; : (384, 384, 384)
voxel&nbsp; &nbsp;: ( 0.5000,&nbsp; 0.5000,&nbsp; 0.5000)
x_(ras) : (-1.0000, -0.0000,&nbsp; 0.0000)
y_(ras) : ( 0.0000, -0.0000, -1.0000)
z_(ras) : ( 0.0000,&nbsp; 1.0000,&nbsp; 0.0000)
c_(ras) : (-2.4468,&nbsp; 9.5993, -9.7705)
file&nbsp; &nbsp; : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgz
Volume Geometry vox2ras
-0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;93.55320;
-0.00000&nbsp; -0.00000&nbsp; &nbsp;0.50000&nbsp; -86.40073;
&nbsp;0.00000&nbsp; -0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;86.22952;
&nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;1.00000;
Volume Geometry vox2ras-tkr
-0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;96.00000;
&nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.50000&nbsp; -96.00000;
&nbsp;0.00000&nbsp; -0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;96.00000;
&nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;1.00000;
cmd[0]: ProgramName: 
mris_remove_intersection&nbsp; ProgramArguments: mris_remove_intersection 
.../surf/lh.orig ../surf/lh.orig&nbsp; ProgramVersion: 7.4.0&nbsp; TimeStamp: 
2023/07/26-08:06:34-GMT&nbsp; BuildTime: May 10 2023 00:12:43&nbsp; BuildStamp:
 freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e&nbsp; User: zhisha&nbsp; 
Machine: linc1&nbsp; Platform: Linux&nbsp; PlatformVersion: 
3.10.0-1160.76.1.el7.x86_64&nbsp; CompilerName: GCC&nbsp; CompilerVersion: 4.8.5
mris_info
creationtime 2023/08/07-23:56:25-GMT
sysname&nbsp; Linux
hostname reslnvhpc0281
machine&nbsp; x86_64
surfacefile lh.white
hemicode&nbsp; &nbsp; 0
talairach_flag&nbsp; 0
rescale&nbsp; &nbsp; &nbsp;0.000000
nvertices&nbsp; &nbsp;159999
nfaces&nbsp; &nbsp; &nbsp; 319994
total_area&nbsp; 98524.593750
group_avg_vtxarea_loaded 0
avgfacearea&nbsp; 0.307895
avgvtxarea&nbsp; 0.615783
avgvtxdist&nbsp; 0.858784
stdvtxdist&nbsp; 0.223460
vtx0xyz&nbsp; &nbsp;-10.953291 -78.142456 0.268743
num_intersecting_faces 255
If I type "mris_info lh.pial", the output is&nbsp;
SURFACE INFO ========================================&nbsp;
type&nbsp; &nbsp; &nbsp; &nbsp; : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 159999
num faces&nbsp; &nbsp;: 319994
num strips&nbsp; : 0
surface area: 119400
vg.valid: 1
AvgFaceArea&nbsp; &nbsp; &nbsp; 0.373132
AvgVtxArea&nbsp; &nbsp; &nbsp; &nbsp;0.746256
AvgVtxDist&nbsp; &nbsp; &nbsp; &nbsp;0.975444
StdVtxDist&nbsp; &nbsp; &nbsp; &nbsp;0.419796
ctr&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: (-34.8974, -3.52912, 26.0063)
original vertex space&nbsp; &nbsp;: surfaceRAS
vertex locs&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;: surfaceRAS
Volume Geometry (vg)
volume geometry:
extent&nbsp; : (384, 384, 384)
voxel&nbsp; &nbsp;: ( 0.5000,&nbsp; 0.5000,&nbsp; 0.5000)
x_(ras) : (-1.0000, -0.0000,&nbsp; 0.0000)
y_(ras) : ( 0.0000, -0.0000, -1.0000)
z_(ras) : ( 0.0000,&nbsp; 1.0000,&nbsp; 0.0000)
c_(ras) : (-2.4468,&nbsp; 9.5993, -9.7705)
file&nbsp; &nbsp; : /project/bbl-bgd/zhisha/yanyang_zhang_7t/S59_VASO/20230308_S59_T01/fs_segmentation/fs_output/mri/wm.mgz
Volume Geometry vox2ras
-0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;93.55320;
-0.00000&nbsp; -0.00000&nbsp; &nbsp;0.50000&nbsp; -86.40073;
&nbsp;0.00000&nbsp; -0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;86.22952;
&nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;1.00000;
Volume Geometry vox2ras-tkr
-0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;96.00000;
&nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.50000&nbsp; -96.00000;
&nbsp;0.00000&nbsp; -0.50000&nbsp; &nbsp;0.00000&nbsp; &nbsp;96.00000;
&nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;0.00000&nbsp; &nbsp;1.00000;
cmd[0]: ProgramName: 
mris_remove_intersection&nbsp; ProgramArguments: mris_remove_intersection 
.../surf/lh.orig ../surf/lh.orig&nbsp; ProgramVersion: 7.4.0&nbsp; TimeStamp: 
2023/07/26-08:06:34-GMT&nbsp; BuildTime: May 10 2023 00:12:43&nbsp; BuildStamp:
 freesurfer-linux-centos7_x86_64-7.4.0-20230510-e558e6e&nbsp; User: zhisha&nbsp; 
Machine: linc1&nbsp; Platform: Linux&nbsp; PlatformVersion: 
3.10.0-1160.76.1.el7.x86_64&nbsp; CompilerName: GCC&nbsp; CompilerVersion: 4.8.5
mris_info
creationtime 2023/08/08-00:01:31-GMT
sysname&nbsp; Linux
hostname reslnvhpc0281
machine&nbsp; x86_64
surfacefile lh.pial
hemicode&nbsp; &nbsp; 0
talairach_flag&nbsp; 0
rescale&nbsp; &nbsp; &nbsp;0.000000
nvertices&nbsp; &nbsp;159999
nfaces&nbsp; &nbsp; &nbsp; 319994
total_area&nbsp; 119400.148438
group_avg_vtxarea_loaded 0
avgfacearea&nbsp; 0.373132
avgvtxarea&nbsp; 0.746256
avgvtxdist&nbsp; 0.975444
stdvtxdist&nbsp; 0.419796
vtx0xyz&nbsp; &nbsp;-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&nbsp;https://secure-web.cisco.com/1ISmWHEli28NnENV_byotaYOAH92Vv6ZabBjx2THy7qNhr5...).
 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" &lt;BFISCHL@mgh.harvard.edu&gt; wrote:
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Hmm, can you try running
&nbsp;
mris_info lh.white
&nbsp;
mris_info lh.pial
&nbsp;
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?
&nbsp;
From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu
 &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp;On Behalf Of&nbsp;DS
Sent:&nbsp;Monday, August 7, 2023 4:00 PM
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;Re: [Freesurfer] Use freeview to visualize white and pial surface
&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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.&nbsp;
PS. the current free RAM is 6GB.
&nbsp;
Best,
Cain
&nbsp;
&nbsp;
At 2023-08-08 03:49:29, "Fischl, Bruce R.,PHD" &lt;BFISCHL@mgh.harvard.edu&gt; 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?
&nbsp;
From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp;On
 Behalf Of&nbsp;DS
Sent:&nbsp;Monday, August 7, 2023 3:48 PM
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;Re: [Freesurfer] Use freeview to visualize white and pial surface
&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Hi expert,
Thanks for your reply. I used the following command line.
freeview -f \
lh.white:edgecolor=blue \
lh.pial:edgecolor=red
&nbsp;
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
&nbsp;
&nbsp;
At 2023-08-08 03:13:52, "Fischl, Bruce R.,PHD" &lt;BFISCHL@mgh.harvard.edu&gt; wrote:
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
What is your freeview command line/
&nbsp;
From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp;On
 Behalf Of&nbsp;DS
Sent:&nbsp;Monday, August 7, 2023 2:51 PM
To:&nbsp;freesurfer@nmr.mgh.harvard.edu
Subject:&nbsp;[Freesurfer] Use freeview to visualize white and pial surface
&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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.
&nbsp;
.../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv:
 Assertion `used_next &lt;= 
save-&gt;vertex_store-&gt;buffer_in_ram_size'
 failed.
&nbsp;
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.&nbsp;
Do you have any thoughts about this issue? Thank you so much for any suggestions.
&nbsp;
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&nbsp;moderator so far.
&nbsp;
Best,
Cain
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Re: [Freesurfer] Use freeview to visualize white and pial surface