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.comwrote:
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 Has it been replaced by a different flag?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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