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 <fis...@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 <fis...@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 >> >> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >>
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