Hi Blue

That message is almost certainly generated by the *.nii bit. Can you path to an actual file instead of a wildcard? If you need multiple inputs you have to give multiple -i options (like -I file1.nii -i file2.nii …)

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ???
Sent: Sunday, September 26, 2021 2:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer V7.1.1: recon-all meet the problem: set: No match

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Dear Freesurfer experts,

I'm a novice in using Freesurfer and I'm trying to run recon-all command to try if I can use Freesurfer to deal with the MRI data. Here is my codes:

"export SUBJECTS_DIR=hcp/data/100206

mkdir -p subject1

recon-all -s sub_try -i T1w/*.nii -sd project/subject1/ -all"

The codes are in quotes, in which 100206 stands for a folder containing T1w folder that have a .nii file, and project stands for the folder I want to store my result.

But when I tried to run this script, I got the feedback "set: No match" and I don't know why.

Could you please give me some suggestions to solve this problem?

Thank you very much!

Best regards,

Blue