Thank you. I have attached the fslerrorreport output
I run the script right in the folder where the anatomical image was, the path being /home/store1/rp729383/Desktop/pilot_scan. The command was fsl_anat -i MPRAGE_pilot2.nii.
-ls -la in the pilot_scan folder gives me the following:
total 11536
drwxr-xr-x. 3 rp729383 CINN_Staff 4096 Nov 27 11:14 .
drwxr-xr-x. 10 rp729383 CINN_Staff 4096 Nov 27 11:13 ..
drwxr-xr-x. 2 rp729383 CINN_Staff 4096 Nov 27 11:14 MPRAGE_pilot2.anat
-rw-r--r--. 1 rp729383 CINN_Staff 11796832 Nov 22 17:16 MPRAGE_pilot2.nii
and in the .anat folder gives me the following:
total 28872
drwxr-xr-x. 2 rp729383 CINN_Staff 4096 Nov 27 11:14 .
drwxr-xr-x. 3 rp729383 CINN_Staff 4096 Nov 27 11:14 ..
-rw-r--r--. 1 rp729383 CINN_Staff 566 Nov 27 11:14 log.txt
-rw-r--r--. 1 rp729383 CINN_Staff 11796832 Nov 27 11:14 T1_fullfov.nii
-rw-r--r--. 1 rp729383 CINN_Staff 5941249 Nov 27 11:14 T1_fullfov.nii.gz
-rw-r--r--. 1 rp729383 CINN_Staff 155 Nov 27 11:14 T1_orig2std.mat
-rw-r--r--. 1 rp729383 CINN_Staff 11796832 Nov 27 11:14 T1_orig.nii
-rw-r--r--. 1 rp729383 CINN_Staff 0 Nov 27 11:14 T1_roi.log
-rw-r--r--. 1 rp729383 CINN_Staff 76 Nov 27 11:14 T1_std2orig.mat
Best,
Christos
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