Freesurfer August 2023

freesurfer@nmr.mgh.harvard.edu

89 participants
126 discussions

Re: [Freesurfer] Use freeview to visualize white and pial surface
by fsbuild 08 Aug '23

08 Aug '23

External Email - Use Caution   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_brZC5MXIy0CPYlNkhR4pAp0qW…; 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 (zkypis(a)126.com) wrote:         External Email - Use Caution         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(a)mgh.harvard.edu> wrote:         External Email - Use Caution         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(a)126.com> wrote:         External Email - Use Caution         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(a)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(a)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/1ISmWHEli28NnENV_byotaYOAH92Vv6ZabBjx2…) 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(a)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(a)nmr.mgh.harvard.edu> On Behalf Of DS Sent: Monday, August 7, 2023 4:00 PM To: Freesurfer support list <freesurfer(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1GO2CxTprXM0WjXwNu3z8MZSD_Kaq9fpHjRhGgnYQQ2kXb… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1GO2CxTprXM0WjXwNu3z8MZSD_Kaq9fpHjRhGgnYQQ2kXb… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1GO2CxTprXM0WjXwNu3z8MZSD_Kaq9fpHjRhGgnYQQ2kXb… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

2 1

Use freeview to visualize white and pial surface
by DS 08 Aug '23

08 Aug '23

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

3 10

followup question on computing merged volumes of both hemispheres
by inbal paran 08 Aug '23

08 Aug '23

External Email - Use Caution By hand/matlab - simply to sum the volumes in each hemisphere? e.g., Rt. Caudate+ Lt. Caudate? ----- You'll have to do it by hand or maybe in matlab; you can use fast_ldtable.m to load in the tables in matlab On 8/5/2023 4:54 AM, inbal paran wrote: External Email - Use Caution Hello FreeSurfer Developers, I need to compute the volume of specific bilateral cortical and subcortical ROIs. I already ran reacon-all on all of my subjects, and I extracted volumes of the ROIs per hemisphere of both the cortical and subcortical brain regions (aseg and aparc). How can I compute the merged volume of both hemispheres per each ROI? The freesurfer version I am using: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1Z9QuT-veibLSEyJxGKDxTdAyAoxIqlB6JWuujOlYgppYXY…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

1 0

Re: [Freesurfer] Freesurfer version and Installation
by fsbuild 08 Aug '23

08 Aug '23

External Email - Use Caution  The mri_synthsr script in the 7.4.1 release from June 2023 offers 3 models - one version 1.0 model and two version 2.0 models (depending upon the arguments).  The default in the absence of any qualifying arguments is the general version 2 model. - R.           if args.v1:             print('Using version 1 model from July 2021')             path_model = os.path.join(os.environ.get('FREESURFER_HOME'), 'models', 'synthsr_v10_210712.h5')          elif args.lowfield:            print('Using model for low-field scans from January 2023 (version 2)')             path_model = os.path.join(os.environ.get('FREESURFER_HOME'), 'models', 'synthsr_lowfield_v20_230130.h5')          else:             print('Using general model from January 2023 (version 2)')             path_model = os.path.join(os.environ.get('FREESURFER_HOME'), 'models', 'synthsr_v20_230130.h5’) On Aug 8, 2023, at 04:52, hmarzban(a)student.ubc.ca wrote:        External Email - Use Caution        Hello,Thank you for your response.I have an additional question: I am utilizing Synthsr version 2.0. Is this particular version included in The 7.4.1 version of freeusrfer?RegardsHengamehFrom: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of hmarzban@student.ubc.ca<hmarzban@student.ubc.ca>Sent: Monday, July 31, 2023 11:38:48 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] Freesurfer version and Installation [CAUTION: Non-UBC Email]        External Email - Use Caution        Dear Freesurfer developers,Previously, I downloaded the freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully analyzed some data using this version. Now, I find myself in the need to reinstall Freesurfer, but I am unable to locate the source file on your website.Could you kindly guide me to where I can find the mentioned version? Alternatively, if this specific version is no longer available, please advise me on which version I should download and install to achieve the same results as before.Thank you very much for your assistance.RegardsHengameh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Freesurfer version and Installation
by hmarzban＠student.ubc.ca 08 Aug '23

08 Aug '23

External Email - Use Caution Dear Freesurfer developers, Previously, I downloaded the freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully analyzed some data using this version. Now, I find myself in the need to reinstall Freesurfer, but I am unable to locate the source file on your website. Could you kindly guide me to where I can find the mentioned version? Alternatively, if this specific version is no longer available, please advise me on which version I should download and install to achieve the same results as before. Thank you very much for your assistance. Regards Hengameh

1 1

Re: [Freesurfer] Calling segmentThalamicNuclei.sh Issue
by fsbuild 07 Aug '23

07 Aug '23

External Email - Use Caution That error is usually from using the wrong shell being used to run a script..  Could you send along the command being used or maybe a screenshot of how it is being run from the terminal ? - R. On Aug 7, 2023, at 07:11, Rowan Lawrence <rowan.lawrence(a)postgrad.manchester.ac.uk> wrote:        External Email - Use Caution        Hello FreeSurfers,I have a student who is trying to run the segmentThalamicNuclei module on some T1 images, using the segmentThalamicNuclei.sh script.All of the subjects have been run through the main recon-all pipeline and each participant has their own folder in the directory which is set to SUBJECTS_DIR containing this output. When calling segmentThalamicNuclei.sh with a subject ID, nothing happens except the following is printed in the terminal: If: Expression syntax.We are assuming that the SUBJECT_ID here corresponds to the name of a participant folder inside of SUBJECTS_DIR containing their recon-all output - is this correct? Is this a syntax error inside of segmentThalamicNuclei.sh, or is there an issue in the way that we are trying to run it?The student is using MacOS Ventura V13.4.1, FreeSurfer V7.4.1, and has the v2019b MATLAB runtime installed. Thank you for any advice!Best wishes,Rowan__________________________________________________________________________________________________GTA/PhD CandidateSchool of Health SciencesZochonis G30, M13 9NT_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Talairach Transform: transforms/talairach.xfm ***FAILED***
by Ha Manh Luu 07 Aug '23

07 Aug '23

External Email - Use Caution Hi Hello FreeSurfer Developers, I Install FS V6.0.0 on Mac OS updated to 12.6.7 and I have the following error when I run recon -all. I also attach tailairach_avi.log and recon-all.log files. Could you help me to fix the bux? #@# Talairach Failure Detection Sat Jul 29 11:35:18 EDT 2023 /Users/hamanhluu/Ha_working/Freesurfer_edit/Test_case_FS/Recon_Pre_T1_source_Mac1/1387/1387_20181219_083728/FreeSurfer/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0018, pval=0.0000 < threshold=0.0050) \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://secure-web.cisco.com/14QnFk2g7tp3Mp1PtQq7sMpaNgFNBZjfVLGW1UVjBu699cT… \nERROR: Talairach failed!\n Darwin MAC198536 21.6.0 Darwin Kernel Version 21.6.0: Thu Jun 8 23:57:12 PDT 2023; root:xnu-8020.240.18.701.6~1/RELEASE_X86_64 x86_64 recon-all -s FreeSurfer exited with ERRORS at Sat Jul 29 11:35:18 EDT 2023 Thank you, Ha

1 0

Bad skull strip
by DS 07 Aug '23

07 Aug '23

External Email - Use Caution Hi expert, I found an issue when I do skull stripping. I used the following command line. recon-all \ -skullstrip \ -s fs_output \ -clean-bm \ -wsthresh 100 But, I found too much brain tissue has been removed, particularly for the visual and motor cortex, please see below. Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include more brain tissues. Looking forward to your reply. Thanks. Best, Cain

2 2

mri_segstats --sbTIVin
by Woo-Suk Tae 07 Aug '23

07 Aug '23

External Email - Use Caution Dear Freesurfer developer. According to the explanation in the https://secure-web.cisco.com/1coHbpSG3RMsDJ9eWWcn4zb_ld9qaPCVetqOo5rL5vuLfQ…, it seems that the TIV volume of SAMSEG pipeline could be added to the aseg.stats with the option of mri_segstats --sbTIVin <sbtiv.stats> ... But, I can not find "--sbTIVin" option in the mri_segstats command of FreeSurfer 7.4.1 or the recent developer version. How can I add sbTIV to aseg.stats? Sincerely yours Woo-Suk, Tae -- ---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: wstae(a)korea.ac.kr, woosuk.tae(a)gmail.com, wo <woostae(a)naver.com>ostae(a)gmail.com ----------------------------------------------------------------------------------------

2 1

Question about group analysis
by inbal paran 07 Aug '23

07 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I have a question regarding group analysis: When I followed the instructions on how to build my FSGD file, it said that:"FSGD files are created automatically by qdec, but qdec is currently (12/9/08) limited to two continuous variables and two discrete variables with two levles. Is this still the case, or is it possible to include more than 2 continuous variables? The freesurfer version I am using: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/10EVZ2XzBNwOtEFs0cIPJQpknExlvtm8Aa2FqcVbk4fO2zM…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

2 1

← Newer
1
...
7
8
9
10
11
12
13
Older →

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2023