Hello Pascal,

What exactly are you trying to achieve?

If you would like to make 001.mgz, then use recon-all -i IM-0001-0001.dcm -s bert.
If you would like to reconstruct the surfaces and the volumes (after doing the first step), try recon-all -s subject -all.

As far as I am concerned, freesurfer is not very good at recognizing spaces. I completely abandoned space keys altogether.

Sincerely,
Ye



On Tue, Jul 9, 2013 at 4:57 PM, Pascal Bou-Haidar <pascalbh@gmail.com> wrote:
Hi Freesurfer users,

I am new to Freesurfer and have run into difficulty with running the recon-all command in terminal on osx. When I type in the command bellow

recon-all  –i  IM-0001-0001.dcm –subject bert –all

I receive

ERROR: Flag i unrecognized.

Also the usage info on recon-all does not list -i as far as I can see. Has it been replaced by a different flag?

On a different note. Has anyone tried to install freesurfer on a second partition with the drive name containing a space character? I have two drives installed on my mac with the second drive foolishly labeled "Second Drive". When I tried to install the bash script  (export and source commands) it ran into trouble recognising the space character between second and drive. I had to change the name to Second_Drive which unfortunately mucks up other apps that use the reference to that original name fine.

Any words of wisdom would be greatly appreciated.

Thanks in advance

Pascal




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