Is this what you meant:
First I tried s0964091@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
s0964091@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 xfgavin@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 janinthesky@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.
s0964091@CRIC-0012
:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
echo $SUBJECTS_DIR Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM s0964091@CRIC-0012
:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
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
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 s0964091@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
s0964091@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 xfgavin@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 janinthesky@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.
s0964091@CRIC-0012
:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
echo $SUBJECTS_DIR Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM s0964091@CRIC-0012
:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
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
also, i think the '/' char is missing before 'home', ie /home/s09....
On Mon, 2010-02-22 at 10:26 -0500, Sita Kakunoori wrote:
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 s0964091@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
s0964091@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 xfgavin@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 janinthesky@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.
s0964091@CRIC-0012
:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
echo $SUBJECTS_DIR Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM s0964091@CRIC-0012
:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
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
freesurfer@nmr.mgh.harvard.edu
-
Janani Dhinakaran -
Nick Schmansky -
Sita Kakunoori