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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/11qUb8_2YtPEBF_9Px0gXhE1NNH4fql9EMxlVlTjefIi07ccxqy2HgKyQ6AaZVOcxA2F0FMQ82cG54nAS0g45-QWGLZGoqbUinfMpKPVi-lUPp1LkrMzY9oHItDh2UgcJngvWyh8GzEbGwAc-y0CgXEqDoH5PmkacXsXNHmXCab_36xMVkuICJK1FSf9eW8dDLQ8F5lUcVlYpqJMbBvSX2kn-v4rI8MgRdsKEHz1W5HDu4bEO-0mm-r62v69sEB6RZlViS_V438eCukY4mempSteuzHTNKCOMHmSMBU3A8iLq14zwqv9g9QkjE7JKDTOgTvLJa9s10P43TYzxDDT4zA/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:
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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
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 <freesurfer@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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