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Dear freesurfer, I am following the installation test as suggested ( http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall/) and am currently stuck at example 2. When I ran recon-all, I got the output: "if: missing file name".
I noticed this has been brought up before, but no solution was provided.
Any suggestions? Thank you.
Kavinash
can you send the command line and full terminal output? Also, when you run it again, put -debug as the first argument. It will create a huge amount of terminal output, but it will be helpful for diagnosing the problem
On 6/2/2019 3:57 AM, Kavinash Loganathan wrote:
External Email - Use Caution
Dear freesurfer, I am following the installation test as suggested (http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall/) and am currently stuck at example 2. When I ran recon-all, I got the output: "if: missing file name".
I noticed this has been brought up before, but no solution was provided.
Any suggestions? Thank you.
Kavinash
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External Email - Use Caution
The problem seems to have been resolved. I began today's session by defining freesurfer home and sourcing the setup script, as suggested. I then re-defined the subjects directory and then ran recon-all -i sample-001.nii.gz -s bert -all. Everything seems fine so far.
I don't really know why this issue happened in the first place, when I simply repeated today what I had done earlier.
Thanks for the assistance and sorry to have taken up your time.
Kavinash
On Sun, 2 Jun 2019 at 23:29, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
can you send the command line and full terminal output? Also, when you run it again, put -debug as the first argument. It will create a huge amount of terminal output, but it will be helpful for diagnosing the problem
On 6/2/2019 3:57 AM, Kavinash Loganathan wrote:
External Email - Use CautionDear freesurfer, I am following the installation test as suggested ( http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall/) and am currently stuck at example 2. When I ran recon-all, I got the output: "if: missing file name".
I noticed this has been brought up before, but no solution was provided.
Any suggestions? Thank you.
Kavinash
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