Hi Jan, Please try rerunning recon-all after removing the spaces or special characters (if there are any) in the dicom files.
Sita. On Mon, 22 Feb 2010, Janani Dhinakaran wrote: > Is this what you meant: > > First I tried > s0964...@cric-0012:~$ recon-all > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > ERROR: Flag > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > unrecognized. > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > 2010 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010 > > Then I tried putting full path in front of both file sets > > > s0964...@cric-0012:~$ recon-all -i > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > -i > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm > -s subj001 > ERROR: cannot find > home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm > Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC > 2010 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010 > > Jan > > > On 22 February 2010 14:30, Xue, Feng <xfga...@gmail.com> wrote: > >> Try with full path, e.g. >> /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >> >> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran >> <janinthe...@gmail.com> wrote: >>> Hello, >>> I ran recon-all on Friday. It ran for around a minute instead of 30-48 >>> hours. Unfortunately, when I try tkmedit and other such commands, the >>> pictures don't visualise. >>> So today I first confirmed that the SUBJECTS_DIR was in Desktop path. >>> (Because over the weekend it had gone back to usr/local... path and so I >>> re-exported it just now.) >>> Then I tried running recon-all again. >>> >>> >>> s0964...@cric-0012 >> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >>> echo $SUBJECTS_DIR >>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM >>> s0964...@cric-0012 >> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ >>> recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i >>> Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001 >>> ERROR: SUBJECTS_DIR >>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not exist. >>> >>> Can anyone help me understand what I can do? >>> Thanks >>> Jan >>> -- >>> I am the Sun, I know no darkness. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> >> >> -- >> Best Regards >> >> Xue, Feng Phd. candidate >> Major in Developmental Cognitive Neuroscience >> >> National Key Laboratory of Cognitive Neuroscience and Learning >> Beijing Normal University >> Beijing, China. 100875 >> Tel: +86-13810154455 >> web: http://psychbrain.bnu.edu.cn >> ============================================== >> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >> telnet://bbs.mdjs.org >> http://bbs.mdjs.org >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
