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/1IMDK1N7QCuFHDBAqbwgRc9pMUoAwzPh8gLV8fwqcUUSZYN... 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.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
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@contbay.com To: freesurfer@nmr.mgh.harvard.edu; Cc: hyejung7890@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/1eD6rhbHoT8I4cLyz7X24S6O3XQl6cfxb1YCJD3aXBmeYvm...
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@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PjIiYHKTPaC4lWLpO5alFqzN6LPLVpF8F0Qae2lmWhBMa6...
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@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@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@contbay.com To: freesurfer@nmr.mgh.harvard.edu; Cc: hyejung7890@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://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macO...https://secure-web.cisco.com/1IMDK1N7QCuFHDBAqbwgRc9pMUoAwzPh8gLV8fwqcUUSZYNUAtkffWnRycsKB-8aNNnZecU30n-LThO_rOXYp_BKdmP4uubAna6GBikj7uoKKAxWfyg0ltpvrbJnznjM8ucu72-EvDBWInryq7Ln74QipZqxLutAiwYkTxTfnUkivop9wJVFh0s1PQ9CtingaAKSC8c7Yk7RwvdfDO1oluWK8W6H2YfS_gGIaXQ0DJ6BnDUBKXr0dWCSg_9I_BURx9B-tLkNE3-Ttz90_Xj_KZDRoeRCc0aktbHn95GmKLFrNW7XWArvn-2qLFEOsyJZmqOFvuxWTt9rNdoUoDXxnUQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
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.krmailto:hyejung7890@amc.seoul..kr To: <freesurfer@nmr.mgh.harvard.edumailto: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@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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1rHpuG797Twv4fdsVdg-_x84n5AbfLpLCt9BGm8LawV8cZofWD9QHGb04TaRvaZmV2YL_2LJNRkzYMApRjiJgQN1yhBz0Ywtfq_0bpnT5ZM-WHXcVNQ39cWMYYM8ZEis6l_Uwg2dN5Kltmrj4feuWXFtAj2Hk8kapxPOMFJnQ2RD1fDdRmVE7g2l0eO80Dgjj7uh-IgAIGA_S8zWDoP9Hvevyr4kO6gdti6OTn-ZU-bSe7val0u19sOoaOEnSITfnZ9wB9Tu4tgTxABkpre3bH4zV8dfrb_K7l51zXmv5XxHC35SP6IjfHPyZLubMWAsjOJfYjX5UUoGzFhxQReFIcQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
[Image removed by sender.]
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@MGH.HARVARD.EDU To: "Freesurfer support list"freesurfer@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@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@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@contbay.com To: freesurfer@nmr.mgh.harvard.edu; Cc: hyejung7890@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/1aULodZcJR9OcolqUFNJTkqilEWkhAZoTQ_Wqep8uMoYj_w...
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@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oge225zSOXkmR4_L9csXLoEtg60I6Bbo60JYaPUMKKQmPO...
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
Huang, Yujing -
윤혜정