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"<fsbu...@contbay.com>
To: <freesurfer@nmr.mgh.harvard.edu>;
Cc: <hyejung7...@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,
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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 <hyejung7...@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: hyejung7...@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
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