External Email - Use Caution
Yup, That solved it! Thank you for your help! I totally missed that. Misque
On Jul 3, 2023, at 9:36 AM, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
External Email - Use Cautionlta_convert looks fine in /Applications/freesurfer/7.4.1/.
Your ‘export FREESURFER_HOME=Applications/freesurfer/7.4.1’ doesn’t have the leading ‘/’.
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Misque Boswell Sent: Monday, July 3, 2023 12:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error Help
External Email - Use CautionThank you, Yujing. Here it is:
Misques-MBP-3 / % /Applications/freesurfer/7.4.1/bin/lta_convert -all-info 7.4.1
ProgramName: lta_convert ProgramArguments: /Applications/freesurfer/7.4.1/bin/lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/07/03-16:28:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: misqueboswell Machine: Misques-MBP-3.local Platform: Darwin PlatformVersion: 22.2.0 CompilerName: Clang CompilerVersion: 12.0.0
Misque
On Jul 3, 2023, at 8:55 AM, Huang, Yujing <YHUANG43@mgh.harvard.edu mailto:YHUANG43@mgh.harvard.edu> wrote:
External Email - Use CautionCan you run the following at prompt?
‘Applications/freesurfer/7.4.1/bin/lta_convert -all-info’
I’m not a Mac user. Do you need ‘/’ in front of ‘Application’?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Misque Boswell Sent: Monday, July 3, 2023 11:44 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error Help
External Email - Use CautionHello Yujing,
Thank you for your response. I followed the directions for setup and sourced SetUpFreeSurfer.sh as you stated. All goes as planned up to this point.
Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1 Misques-MBP-3 / % 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 FSL_DIR /Users/misqueboswell/fsl
Can you check where your recon-all is and if lta_convert is in the distribution?
- which recon-all
Misques-MBP-3 / % which recon-all Applications/freesurfer/7.4.1/bin/recon-all
- ls -l <recon-all_path>/lta_convert
lta_convert executable is in the "Applications/freesurfer/7.4.1/bin/" (rwxr-xr-x 1 root wheel 2613752 Jun 13 21:21 lta_convert)
Thank you again for your help! Misque
On Jul 3, 2023, at 6:26 AM, Huang, Yujing <YHUANG43@mgh.harvard.edu mailto:YHUANG43@mgh.harvard.edu> wrote:
Yujing
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