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 (hyejung7...@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"<yhuan...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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"<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, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16QsjI_IFOK8Xo0B1gMl3uWmO7oo4wVgTL1WN7x8nR916ZXpeDKxxuAWopZIjbfqH72qVw4Ms5TqQNmSvrAeAYV_mOKhiwg0yIYNx8fsLKI-nL7x3tgxF3-2bl0EIwA2SBk-At_d1hnfHcIEMYX8crxT7XRLsiknyl8FOQGRAGE4ToF4KANVZoZe6cLpfQ-CrV_EnA1KG9AIAJm9_wfyCQ7DF_YvNwdxGTGTgWPThn7eL2JLYtrb8A7rCmFbhjnPn1gA5y1_SzPvM2BfefpFMSwZrY8lMB68UFHpUvkWy-YdmWhYqq7jjo01KKnfXS1weRikAyDcnqCNx5nwpw3r5tQ/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 <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. 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