On 22 February 2010 16:27, Janani Dhinakaran <janinthe...@gmail.com> wrote:
> When I set SUBJECTS_DIR to /Desktop/..... I get this > > s0964...@cric-0012:~$ export > SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > s0964...@cric-0012:~$ echo $SUBJECTS_DIR > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ > > Which makes it part of home anyway. > > When I add home into the path I get a double- > > s0964...@cric-0012:~$ export > SUBJECTS_DIR=~/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > s0964...@cric-0012:~$ echo $SUBJECTS_DIR > > /home/s0964091/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM > > And the Recon-all has errors too. > > > s0964...@cric-0012:~$ 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.d > ERROR: cannot find > /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.d > > 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 16:24:46 GMT 2010 > > > It doesn't run recon at all. Unlike the previous command which did but > incompletely. > > Jan > > > > On 22 February 2010 16:21, Xue, Feng <xfga...@gmail.com> wrote: > >> It seems that your problem is the recon-all script couldn't find your >> SUBJECTS_DIR, possibly because you didn't give it full path. So I >> suggest to try define SUBJECTS_DIR as >> /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM, >> then rerun your recon-all command as before. >> >> On Mon, Feb 22, 2010 at 10:44 PM, Janani Dhinakaran >> <janinthe...@gmail.com> 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 >> > >> > >> > >> > -- >> > I am the Sun, I know no darkness. >> > >> >> >> >> -- >> 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 >> > > > > -- > I am the Sun, I know no darkness. > -- 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
