Dear freesurfer exports,

I still have the problem to recon the surface with more than 10 inputs from one person with following command:

“recon-all -s ${subjec}  -autorecon1 ?Cnotal-check -clean-bm -gcut -no-isrunning -noappend”,

Is there a limit on the number of the inputs?

What is the algorithm applied by “recon-all” to average these images? Is it viable to average input images with other methods, then apply “recon-all” to the averaged result?

Thanks very much for your help!

Dong Haoming

发件人: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] 代表 董昊铭
发送时间: 2015年11月26日 13:11
收件人: freesurfer@nmr.mgh.harvard.edu
主题: [Freesurfer] recon-all with more than 10 inputs

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