On 22 February 2010 16:27, Janani Dhinakaran janinthesky@gmail.com wrote:
When I set SUBJECTS_DIR to /Desktop/..... I get this
s0964091@CRIC-0012:~$ export SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/ s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/
Which makes it part of home anyway.
When I add home into the path I get a double-
s0964091@CRIC-0012:~$ export SUBJECTS_DIR=~/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR
/home/s0964091/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
And the Recon-all has errors too.
s0964091@CRIC-0012:~$ 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.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 xfgavin@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 janinthesky@gmail.com 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
-- 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.
freesurfer@nmr.mgh.harvard.edu
-
Janani Dhinakaran