On 4 September 2012 14:37, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

if that's the name of the image file. Can you post the list on your replies so others can answer?

thanks
Bruce

On Tue, 4 Sep 2012, Varghese Chikku wrote:

Hi Bruce,
Many thanks for  you mail.
Is this the  command  you referring to.
recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid test4
Thanks
Chikku

On 3 September 2012 17:33, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      Hi Chikku

      you need to give it the path to an image file (any one will do) and it will figure out the other slices that makeup
      the same series. What is the resolution of your data? 50 slices isn't usually enough to cover the brain at high
      enough resolution to get good thickness results.

      cheers
      Bruce


      On Mon, 3 Sep 2012, Varghese Chikku wrote:

             
            Hi,
             
            While running the following command:

            recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2

            I keep seeing the following error:

            ...

            corRead(): can't open file
            /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info
            $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
            reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre...
            Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
            2009 i686 GNU/Linux
            recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012


            My image files, in dcm format, are at
            /media/sf_freesurferstudys/raw/raw_scr/T1pre :

            /media/sf_freesurferstudys/raw/raw_scr/T1pre> ls
            Image00001  Image00010 Image00019  Image00028 Image00037  Image00046
            Image00002  Image00011 Image00020  Image00029 Image00038  Image00047
            Image00003  Image00012 Image00021  Image00030 Image00039  Image00048
            Image00004  Image00013 Image00022  Image00031 Image00040  Image00049
            Image00005  Image00014 Image00023  Image00032 Image00041  Image00050
            Image00006  Image00015 Image00024  Image00033 Image00042
            Image00007  Image00016 Image00025  Image00034 Image00043
            Image00008  Image00017 Image00026  Image00035 Image00044
            Image00009  Image00018 Image00027  Image00036 Image00045

             Many thanks for  your help.
            chikku




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