Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 discussions

Re: [Freesurfer] ERROR: could not configure recon-all parameters
by fsbuild 15 Oct '23

15 Oct '23

External Email - Use Caution   Just FYI, it is not intended that you process your own subjects using SUBJECTS_DIR set to a path under where freesurfer is installed, i.e., SUBJECTS_DIR in the log is set to, setenv SUBJECTS_DIR /Applications/freesurfer/subjects/recon-all cd /Applications/freesurfer/subjects/recon-all/MR7312_501/surf Writing files there normally fail without the sudo command, % touch /Applications/freesurfer/foo touch: /Applications/freesurfer/foo: Permission denied That will prevent recon-all from being able to create soft links.  Neither should recon-all be run with the sudo command or that path down-protected to allow writing files there w/o the sudo command. After the setup of the freesurfer environment with, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.4.1 FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects MNI_DIR           /Applications/freesurfer/7.4.1/mni - then change SUBJECTS_DIR to point to a directory where you already have write permission like somewhere under your home directory, $ cd $HOME $ pwd /Users/<your userid> $ mkdir -p $HOME/subjects .... and reset SUBJECTS_DIR to point to the path you just made ... $ export SUBJECTS_DIR=$HOME/subjects $ echo $SUBJECTS_DIR /Users/<your userid>/subjects Then try running your commands. - R. On 10/15/23 20:19, 윤혜정 (hyejung7890(a)amc.seoul.kr) wrote:         External Email - Use Caution         Hi Yujing,  Thank you for your help. I see it works now. I have attached my recon-all log for you to see. Can you please go through it and confirm that it has no errors?  Thank you.  Best,Alice -----Original Message----- From: "Huang, Yujing"<YHUANG43(a)MGH.HARVARD.EDU> To: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; Cc: Sent: 2023. 10. 13. (금) 20:54 (GMT+09:00) Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters   lh.pial and rh.pial are created as symbol links to lh.pial.T1 and rh.pial.T1. rh.pial -> rh.pial.T1 lh.pial -> lh.pial.T1   Do you have lh.pial.T1 and rh.pial.T1 in your surf/ directory?  Symbol links may be disallowed for your machine. Can you attach recon-all.log?   Best,   Yujing   From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh..harvard.edu> On Behalf Of ??? Sent: Thursday, October 12, 2023 9:32 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters           External Email - Use Caution         Thank you for your swift reply. I will try that soon.   I have other pack of data that finished recon-all process and I don't have lh-pial & rh-pial to view on freeview for some reason. I have the same problem for all of recon'd files.  Is this another recon-all error or is this just my data problem?    Thank you in advance.   Best, Alice   -----Original Message----- From: "fsbuild"<fsbuild(a)contbay.com> To: <freesurfer(a)nmr.mgh.harvard.edu>; Cc: <hyejung7890(a)amc.seoul.kr>; Sent: 2023. 10. 13. (금) 10:04 (GMT+09:00) Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters           External Email - Use Caution           It looks like permissions on the installed freesurfer files and/or what you set FREESURFER_HOME to may not be correct.   I would delete your current freesurfer install and then use the Mac installer package (.pkg) file to install the 7.4.1 release.  That should ensure all the file privileges are correct so the files can be executed.  You will need sudo privileges for these commands.   … open a terminal window and delete the current freesurfer installation …   $ cd /Applications $ sudo  rm -rf freesurfer … you will be asked to enter your password ... $ cd   Download the 7.4.1 package installer in your browser using the link, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16QsjI_IFOK8Xo0B1gMl3uWmO7oo4wVgTL1WN7x8nR916Z…   In a Finder window, open your downloads folder (or go to wherever you downloaded the .pkg file).  Then RIGHT CLICK with the mouse on the icon for the file freesurfer-macOS-darwin_x86_64-7.4.1.pkg and select “Open With” installer.app (default).   Select “Open” when the installer opens a new window asking if you want to do the install.  Click thru the installer options by selecting “Continue” and accept the license, etc.   … when the install is done, setup the Fresurfer environment in a terminal window …   $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.4.1 FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects MNI_DIR           /Applications/freesurfer/7.4.1/mni   … check python3 is there ...   $ ls $FREESURFER_HOME/python/bin/python3 /Applications/freesurfer/7.4.1/python/bin/python3   … then try running freesurfer commands again …   - R.   On Oct 12, 2023, at 20:01, 윤혜정 <hyejung7890@amc.seoul..kr> wrote:           External Email - Use Caution         Hi,     On top of the email I sent earlier, I also get the next error line that says:   ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file  /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0     -----Original Message----- From: hyejung7890@amc.seoul.kr To: <freesurfer@nmr.mgh.harvard.edu>;  Cc:  Sent: 2023. 10. 13. (금) 08:35 (GMT+09:00) Subject: ERROR: could not configure recon-all parameters   Good day,    I get the following error message when I run recon-all:   ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file    I went through a bit of the mail archive and unlike the others I don't see ASCII error message in mine.    Additionally, I was wondering if the thickness of MR slices would affect recon-all process at all?    I appreciate your help.    Best wishes, Alice  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1EiGLGKIpO0RoPRKb_RBjd80W6iWP0i6qsrSn5C6agnsky…     _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/156_ldS1A-KRmiP3d3DdvfNZ1_ZpwzQDZecZYZHt2mlVDS… 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.

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Re: [Freesurfer] ERROR: could not configure recon-all parameters
by fsbuild 15 Oct '23

15 Oct '23

External Email - Use Caution  It looks like permissions on the installed freesurfer files and/or what you set FREESURFER_HOME to may not be correct. I would delete your current freesurfer install and then use the Mac installer package (.pkg) file to install the 7.4.1 release.  That should ensure all the file privileges are correct so the files can be executed.  You will need sudo privileges for these commands. … open a terminal window and delete the current freesurfer installation … $ cd /Applications$ sudo  rm -rf freesurfer… you will be asked to enter your password ...$ cd Download the 7.4.1 package installer in your browser using the link, https://secure-web.cisco.com/1IMDK1N7QCuFHDBAqbwgRc9pMUoAwzPh8gL… In a Finder window, open your downloads folder (or go to wherever you downloaded the .pkg file).  Then RIGHT CLICK with the mouse on the icon for the file freesurfer-macOS-darwin_x86_64-7.4.1.pkg and select “Open With” installer.app (default).   Select “Open” when the installer opens a new window asking if you want to do the install.  Click thru the installer options by selecting “Continue” and accept the license, etc. … when the install is done, setup the Fresurfer environment in a terminal window … $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.4.1 FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects MNI_DIR           /Applications/freesurfer/7.4.1/mni … check python3 is there ... $ ls $FREESURFER_HOME/python/bin/python3/Applications/freesurfer/7.4.1/python/bin/python3 … then try running freesurfer commands again … - R. On Oct 12, 2023, at 20:01, 윤혜정 <hyejung7890(a)amc.seoul.kr> wrote:        External Email - Use Caution        Hi,  On top of the email I sent earlier, I also get the next error line that says: ERROR: could not configure recon-all parameters/Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0 -----Original Message-----From: hyejung7890@amc.seoul.krTo: <freesurfer@nmr.mgh.harvard.edu>; Cc: Sent: 2023. 10. 13. (금) 08:35 (GMT+09:00)Subject: ERROR: could not configure recon-all parameters Good day,  I get the following error message when I run recon-all: ERROR: could not configure recon-all parameters/Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file I went through a bit of the mail archive and unlike the others I don't see ASCII error message in mine.  Additionally, I was wondering if the thickness of MR slices would affect recon-all process at all?  I appreciate your help.  Best wishes,Alice _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] data quality check before analysis [EXTERNAL]
by John Anderson 14 Oct '23

14 Oct '23

External Email - Use Caution It doesn't matter, just make sure to be consistent. Use the same system, the same computer setup, and the same system version, etc. Analyzing data in parallel is always recommended with large sample sizes like yours ** External Email - Caution ** External Email - Use Caution Thank you for your response. My next question is regarding the analysis process. I am curious to know if there is any difference between analyzing one specific subject and analyzing multiple subjects in parallel. For instance, if I am working on 1000 subjects, would it make a difference in the volumetric results if I analyze all of them at once in parallel or break them down into smaller groups to analyze? I would greatly appreciate your help with this. Thank you and Best Regards, Yunus. -------------------------------------------------------------------------------- *Yunus Soleymani* *Ph.D. Candidate of Neuroimaging * *Tehran University of Medical Sciences* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com <https://secure-web.cisco.com/1WPH5Bt5uc1Xj85aTfwm7Tr06k7_Axb61TjUsuWsj9AshI…>* +98 914 526 9298 -------------------------------------------------------------------------------- On Saturday, October 14, 2023 at 03:29:11 PM GMT+3:30, John Anderson < jb19790001(a)gmail.com> wrote: External Email - Use Caution - FreeSurfer 5.3 QA Tools *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1pVeXzPnGpx6B2fKOoBmW3MHav95756yrRMgP7HJh6IJKU… <https://secure-web.cisco.com/1X4SVtjfuS9P5wjtYNSZeaPs3CnIXR07prqwkfcNvWh2rB…> - For versions 7+, use the following executable to compute QA stats *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1jd8feriFIfOfhz3QosHn2W2rk3OOeZUuj0X0RpNnshuDm… <https://secure-web.cisco.com/1sirjJxRdaG_LwsFc9BxcTnKi2u4q_K765ccWgFzszfd7x…> Be aware that there are NO alternatives to visual inspection ------------------------------ *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu < freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of yunus soleymani < soleymani.yunus(a)yahoo.com> *Sent:* Saturday, October 14, 2023 3:18 AM *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* [Freesurfer] data quality check before analysis [EXTERNAL] ** External Email - Caution ** External Email - Use Caution Hi there, My name is Yunus and I'm currently working on my Ph.D. thesis, which involves analyzing the HCP database volumetrically using Freesurfer. However, before I begin with the software, I was wondering if there is a tool in Freesurfer that can perform a quality check on the data to identify any possible artifacts or noise that might affect the analysis. Could you please let me know if such a tool exists in Freesurfer? Your help would be much appreciated. Thank you and Best Regards, Yunus. -------------------------------------------------------------------------------- *Yunus Soleymani* *Ph.D. Candidate of Neuroimaging * *Tehran University of Medical Sciences* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com <https://secure-web.cisco.com/1vR7NCYmqBwGE_G8pzm1u82Wa_EkUO5zL8AcqJzRj5XPND…>* +98 914 526 9298 -------------------------------------------------------------------------------- _______________________________________________ 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/1haxXPzY_I0BGLDjCxf2uKz9gKd9jpou3A2vDk8WYiMt12… <https://secure-web.cisco.com/1R42Zu57Lh2ZvzuP-BHxA2Q7hjwvnWPHFvBQsA_eHbGGLl…>

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Freeview misaligned surfaces "warning matrixinverse failed"
by Andrei Bieger 14 Oct '23

14 Oct '23

External Email - Use Caution Hi, all! I had to reinstall my VM where I had freesurfer running. Everything was running fine before. It is now a VirtualBox VM running Ubuntu 20.04 on my Windows laptop, where I'm running the version 7.4.1 of Freesurfer. When I downloaded freesurfer it wouldn't run freeview, with the following output: "Application failed to start because no Qt platform plugin could be initialized. Available plugins are: (...)" After some research, I tried "sudo apt install qt5-default" and freeview started running. But the thing is, every time I try loading a subject, the surfaces get completely misaligned with the volumes and the following messages show on the terminal: "Warning: MatrixInverse failed" and "Did not find any volume info". Please, see attached image. [image: Screenshot from 2023-10-14 15-06-44.png] I tried using Ubuntu 22 and previous versions of freesurfer but the problem persisted. I also found a message with a similar issue on this list, but the user stopped answering so a solution wasn't proposed. There is also a release note from v5.3.0 saying that on Fedora this message would come up, but this is not the case. Any help with that? -- Andrei Bieger

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Re: [Freesurfer] data quality check before analysis [EXTERNAL]
by John Anderson 14 Oct '23

14 Oct '23

External Email - Use Caution - FreeSurfer 5.3 QA Tools https://secure-web.cisco.com/1xhhgMhrQlSBmGkb8NMn06KLlNRaz3DnQ7vzdZdQzrqjoe… - For versions 7+, use the following executable to compute QA stats https://secure-web.cisco.com/176EEDJE8rR684nmHeoPJAc8XhajsuDydGl4DaVSEQrq7S… Be aware that there are NO alternatives to visual inspection ------------------------------ *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu < freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of yunus soleymani < soleymani.yunus(a)yahoo.com> *Sent:* Saturday, October 14, 2023 3:18 AM *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* [Freesurfer] data quality check before analysis [EXTERNAL] ** External Email - Caution ** External Email - Use Caution Hi there, My name is Yunus and I'm currently working on my Ph.D. thesis, which involves analyzing the HCP database volumetrically using Freesurfer. However, before I begin with the software, I was wondering if there is a tool in Freesurfer that can perform a quality check on the data to identify any possible artifacts or noise that might affect the analysis. Could you please let me know if such a tool exists in Freesurfer? Your help would be much appreciated. Thank you and Best Regards, Yunus. -------------------------------------------------------------------------------- *Yunus Soleymani* *Ph.D. Candidate of Neuroimaging * *Tehran University of Medical Sciences* *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com <https://secure-web.cisco.com/1b4Zahk7jmAyrHinzKCHjz95tCDKjVy_xhMBgqvGUqfyvQ…>* +98 914 526 9298 --------------------------------------------------------------------------------

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data quality check before analysis
by yunus soleymani 14 Oct '23

14 Oct '23

External Email - Use Caution Hi there, My name is Yunus and I'm currently working on my Ph.D. thesis, which involves analyzing the HCP database volumetrically using Freesurfer. However, before I begin with the software, I was wondering if there is a tool in Freesurfer that can perform a quality check on the data to identify any possible artifacts or noise that might affect the analysis. Could you please let me know if such a tool exists in Freesurfer? Your help would be much appreciated. Thank you and Best Regards,Yunus. --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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Convert in subject space after cw256
by Maurilio Genovese 13 Oct '23

13 Oct '23

External Email - Use Caution Hi all, I am trying to convert freesurfer reconall output back in original subject space so I am following this guide: https://secure-web.cisco.com/1gX-L0rMewLeZ04f3aHxi6QsxMjCpOru8m6oGdCmStPD1u… However some of my images have a very large fov so I use the cw256 option. In those cases converting back results in rawavg.mgz is not enough, because the fov of rawavg.mgz is already downscaled, so I think I need to go back to 001.mgz. Can someone help me to understand how to go from the cw256 cropped space to the original space? Thanks Maurilio

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(no subject)
by Maurilio Genovese 13 Oct '23

13 Oct '23

External Email - Use Caution Hi all, I am trying to convert freesurfer reconall output back in original subject space so I am following this guide: https://secure-web.cisco.com/1hdoEYpcNfh6v9Yoq-8Iexo7oO3DXo3uI45KMmpjSSOcdu… However some of my images have a very large fov so I use the cw256 option. In those cases converting back results in rawavg.mgz is not enough, because the fov of rawavg.mgz is already downscaled, so I think I need to go back to 001.mgz. Can someone help me to understand how to go from the cw256 cropped space to the original space? Thanks Maurilio

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Re: [Freesurfer] ERROR: could not configure recon-all parameters
by 윤혜정 12 Oct '23

12 Oct '23

External Email - Use Caution Hi, On top of the email I sent earlier, I also get the next error line that says: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0 -----Original Message----- From: hyejung7890(a)amc.seoul.kr To: <freesurfer(a)nmr.mgh.harvard.edu>; Cc: Sent: 2023. 10. 13. (금) 08:35 (GMT+09:00) Subject: ERROR: could not configure recon-all parameters Good day, I get the following error message when I run recon-all: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file I went through a bit of the mail archive and unlike the others I don't see ASCII error message in mine. Additionally, I was wondering if the thickness of MR slices would affect recon-all process at all? I appreciate your help. Best wishes, Alice

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ERROR: could not configure recon-all parameters
by 윤혜정 12 Oct '23

12 Oct '23

External Email - Use Caution Good day, I get the following error message when I run recon-all: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file I went through a bit of the mail archive and unlike the others I don't see ASCII error message in mine. Additionally, I was wondering if the thickness of MR slices would affect recon-all process at all? I appreciate your help. Best wishes, Alice

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Freesurfer October 2023