Hi,
I started to run an old subject through autorecon1 and 2. I used the -legacy flag. However, I still got the error below, saying that I need some *mgz files in the orig/ directory. I thought -legacy would do this conversion.
The orig/ had a COR volume, but the error said to have a 001.mgz and a 002.mgz. I tried to convert the dicoms with -i, but it would not write to the existing directory:
recon-all -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21527384 -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21526253 -subjid CARG29_recon INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS ERROR: /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon exists
So, I ended up converting the dicoms in another directory, copied the 001.mgz and 002.mgz to the CARG29_recon/, and then started to run recon-all -autorecon1 and 2. Is there a simpler way to do this?
Thanks, Vasanth
[biggs:mri] (nmr-dev-env) recon-all -subjid CARG29_recon -autorecon1 -autorecon2 INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev -rwxrwx--- 1 vasanthp cagn 76436 Feb 13 16:22 /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/scripts/recon-all.log Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/dev Previous: /space/windu/6/users/freesurfer_cenagn/freesurfer_dev #-------------------------------------------- #@# MotionCor Mon Feb 13 16:23:34 EST 2006 ERROR: no run data found in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri. Make sure to have a volume called 001.mgz in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Feb 13 16:23:34 EST 2006
Hi Vasanth,
The command-line below does not have -legacy
[biggs:mri] (nmr-dev-env) recon-all -subjid CARG29_recon
-autorecon1 -autorecon2
Also, please remember to follow the bug reporting guidlines in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
doug
Vasanth Pappu wrote:
Hi,
I started to run an old subject through autorecon1 and 2. I used the -legacy flag. However, I still got the error below, saying that I need some *mgz files in the orig/ directory. I thought -legacy would do this conversion.
The orig/ had a COR volume, but the error said to have a 001.mgz and a 002.mgz. I tried to convert the dicoms with -i, but it would not write to the existing directory:
recon-all -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21527384 -i /autofs/space/solo_004/users/dcm/CARG29/cdrom/03051411/21526253 -subjid CARG29_recon INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS ERROR: /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon exists
So, I ended up converting the dicoms in another directory, copied the 001.mgz and 002.mgz to the CARG29_recon/, and then started to run recon-all -autorecon1 and 2. Is there a simpler way to do this?
Thanks, Vasanth
[biggs:mri] (nmr-dev-env) recon-all -subjid CARG29_recon -autorecon1 -autorecon2 INFO: SUBJECTS_DIR is /autofs/space/biggs_008/users/vasanthp/NHS Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev -rwxrwx--- 1 vasanthp cagn 76436 Feb 13 16:22 /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/scripts/recon-all.log
Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/dev Previous: /space/windu/6/users/freesurfer_cenagn/freesurfer_dev #-------------------------------------------- #@# MotionCor Mon Feb 13 16:23:34 EST 2006 ERROR: no run data found in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri. Make sure to have a volume called 001.mgz in /autofs/space/biggs_008/users/vasanthp/NHS/CARG29_recon/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux biggs 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 14:49:37 CDT 2005 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Feb 13 16:23:34 EST 2006
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Vasanth Pappu