Hi Ankita
you need to give recon-all a directive like -all. Also, give it the minc file as input with -i /Sample1/subjects/t1/t1xxxx.mnc
cheers Bruce On Sun, 24 Jan 2016, Arindam Chatterjee wrote:
Hello Freesurfer experts,I am still learning various aspects of Freesurfer, so pardon my questions. I am trying to run recon-all on a mnc file. It is in a folder such as /Sample1/subjects/t1/t1xxxx.mnc. I am pointing my SUBJECTS_DIR to /Sample1/subjects. But when I run recon-all -s t1, I get and error - ERROR: nothing to do. Should I be storing the .mnc file in a different location?
So it looks like it is not finding the .mnc file or can Freesurfer not process a .mnc file and I have to convert it to another format like .dcm? Also, if I am able to run recon-all, what output should I analyze to determine the gyrification index?
Thanks in advance for any pointers.
Ankita
Arindam Chatterjee(515) 419-7384 www.linkedin.com/in/chatterjeea