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:
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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
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