Dear freesurfer exports,

I am trying to recon more than 10 T1 scans from a single subject, but something went wrong.

I have converted all T1 nifti files into mgz format into mri/orig directory with following names: 001.mgz 002.mgz …. 010.mgz 011.mgz… But when I run the command:

“recon-all ?Cs ${subjec} ?Cautorecon1 ?Cnotal?Ccheck ?Cclean-bm ?Cgcut ?Cno-isrunning -noappend”,

it seems that recon-all only recognizes the files with names 01*.mgz(i.e. 0013.mgz), the 00*.mgz(i.e. 001.mgz) files failed to be processed. Once I change the files name to “001.mgz 002.mgz …. 0010.mgz 0011.mgz”, the 00*.mgz(i.e. 001.mgz) are able to be recognized, but the 001*.mgz(i.e. 0013.mgz) files failed.

How should I deal with this to make all files recognized?

Sincerely,

Dong Haoming