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
External Email - Use Caution
What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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" BFISCHL@mgh.harvard.edu wrote:
External Email - Use Caution
What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
External Email - Use Caution What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 2:51 PM To: freesurfer@nmr.mgh.harvard.edumailto: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
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" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@mgh.harvard.edu wrote:
External Email - Use Caution
What is your freeview command line/
From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 3:48 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
External Email - Use Caution What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 2:51 PM To: freesurfer@nmr.mgh.harvard.edumailto: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
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_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 (https://secure-web.cisco.com/1Tka8LRtDcap9tgmBctplaTeza5QjcjT3cXFZbPTxZl_LMM... ). 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" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@mgh.harvard.edu wrote:
External Email - Use Caution
What is your freeview command line/
From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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 <zkypis@126.commailto:zkypis@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_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/1AywoNNFsM5mG0fJ-ZLZwi3PG-TBovTpBhtyJsckDOWYBAz...https://secure-web.cisco.com/1Tka8LRtDcap9tgmBctplaTeza5QjcjT3cXFZbPTxZl_LMM4pF1qyduf4DU-qSM3Rek2_RA5AdtEPpvnOj9Jy170ZUwjM-80H_YZ8HPkjiBLdbWB8F4CzExKNj-05T6IwvkUzHuRYVfkHNS6FWInci_csyMT5kCUNJh3lz6BS2TxUmEK63WzCglLO9jT09CaFT9Ror764bKFGIjIRxMGqfAUZHpNFtBxYJ-yzLuVXrE3MY4lfhXyM04TQ5ZuAvVu_sWOkjk-etW17L0JVxrXs0Pt3-L3Yr_WxcTpxMV7WbY8WxZRWDQnwKj7ozUybUBtt5rRTzgKqC2tRmoRB0dF3eg/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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 4:00 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 3:48 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
External Email - Use Caution What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 2:51 PM To: freesurfer@nmr.mgh.harvard.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pQMiOr5SyATt5_69dvBc-K6cRvgr2SA50jcii0hfar84Gi...
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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" RWANG4@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 zkypis@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_9Px0gXhE1NNH4fql9EMxlVlTjefIi07c... ). 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" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@mgh.harvard.edu wrote:
External Email - Use Caution
What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gnAiU-qsxE90wl1ENbyTHrPgiYiv7SriVrRElAVJJv7LFo...
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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 <zkypis@126.commailto:zkypis@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" <RWANG4@mgh.harvard.edumailto:RWANG4@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 <zkypis@126.commailto:zkypis@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/1N3j9RGrKOGBd5JURf1pzXRj5VeO4hIxol1uJ3jq4RdIwOl...https://secure-web.cisco.com/1Tka8LRtDcap9tgmBctplaTeza5QjcjT3cXFZbPTxZl_LMM4pF1qyduf4DU-qSM3Rek2_RA5AdtEPpvnOj9Jy170ZUwjM-80H_YZ8HPkjiBLdbWB8F4CzExKNj-05T6IwvkUzHuRYVfkHNS6FWInci_csyMT5kCUNJh3lz6BS2TxUmEK63WzCglLO9jT09CaFT9Ror764bKFGIjIRxMGqfAUZHpNFtBxYJ-yzLuVXrE3MY4lfhXyM04TQ5ZuAvVu_sWOkjk-etW17L0JVxrXs0Pt3-L3Yr_WxcTpxMV7WbY8WxZRWDQnwKj7ozUybUBtt5rRTzgKqC2tRmoRB0dF3eg/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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 4:00 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 3:48 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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" <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote:
External Email - Use Caution What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 2:51 PM To: freesurfer@nmr.mgh.harvard.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1thzR-Nl4cFre4rFN3w9-5vhNKBuKDt0EHj2YXeTztUe-KG...https://secure-web.cisco.com/1pQMiOr5SyATt5_69dvBc-K6cRvgr2SA50jcii0hfar84GivjxLNoY9kB3eZn1WTJmM1yGU9FfD9Ml4hDPHtuhhKaa63z8jfl4iZegWcx7Bnv6uySW3dOQFdf0ui8SBEwYiWJrntiChbb52-cOLNl_7XrN3211hYYLkEgrydHZvV4qLk8XY04iTnxrZEcwxzsBcYFWjYkhiUZxVciovDvFRy8SFuWOp9-9_yUHxqrIWhmj5PQc-RtLzgxM682J8U7KU_8BVQKjfTNZiFJQYKR5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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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" RWANG4@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 zkypis@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" RWANG4@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 zkypis@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/1cLz1DHmnHMB9vrzC-_LA_xXaAA8gTpbCs7RyQDLWaTJWhn... ). 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" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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" BFISCHL@mgh.harvard.edu wrote:
External Email - Use Caution
What is your freeview command line/
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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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DS -
Fischl, Bruce R.,PHD -
Wang, Ruopeng