Thanks Bruce,

Still no luck,this what I am getting

/freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0

Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0

INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects

Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

/home/virtualuser/freesurfer/subjects/test7

mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz

mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz

file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm

Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012

For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FreeSurfer:~/freesurfer/subjects/test1>

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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