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Hi,
we have only 1 orig.mgz file, so motion correction is not required. In this case, it would be ideal if recon-all auto-detected or at least had an option to skip motion correction. As it is, it fails entirely when no 001.mgz file exists. I have a file called orig.mgz, should it be renamed to 001.mgz even though there is no 002.mgz?
endorphin.32> ls -l ucsf_disc01/mri/orig/ total 5784 - -rw-rw-rw- 1 dweber dnl 5907576 May 3 13:52 orig.mgz
endorphin.31> recon-all -subjid ucsf_disc01 -all INFO: SUBJECTS_DIR is /data/dnl-raid2/freesurfer/subjects Actual FREESURFER_HOME /data/dnl-raid1/freesurfer - -rw-rw---- 1 dweber dnl 56553 May 3 13:55 /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/scripts/recon-all.log Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux WM removal version #-------------------------------------------- #@# MotionCor Wed May 3 13:55:54 PDT 2006 ERROR: no run data found in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri. Make sure to have a volume called 001.mgz in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/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 endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed May 3 13:55:54 PDT 2006
Thanks, Darren
- --
Darren L. Weber, Ph.D. Postdoctoral Scholar
Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA.
Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber
"To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)
Yes, when you first start, the only volumes that should be there are orig/RRR.mgz. This is the only situation in which recon-all will work from begining to end (unless you use -i to spec the inputs). It will autodetect that there is only one volume and then skip the mc.
doug
Darren Weber wrote:
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Hi,
we have only 1 orig.mgz file, so motion correction is not required. In this case, it would be ideal if recon-all auto-detected or at least had an option to skip motion correction. As it is, it fails entirely when no 001.mgz file exists. I have a file called orig.mgz, should it be renamed to 001.mgz even though there is no 002.mgz?
endorphin.32> ls -l ucsf_disc01/mri/orig/ total 5784
- -rw-rw-rw- 1 dweber dnl 5907576 May 3 13:52 orig.mgz
endorphin.31> recon-all -subjid ucsf_disc01 -all INFO: SUBJECTS_DIR is /data/dnl-raid2/freesurfer/subjects Actual FREESURFER_HOME /data/dnl-raid1/freesurfer
- -rw-rw---- 1 dweber dnl 56553 May 3 13:55
/data/dnl-raid2/freesurfer/subjects/ucsf_disc01/scripts/recon-all.log Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux WM removal version #-------------------------------------------- #@# MotionCor Wed May 3 13:55:54 PDT 2006 ERROR: no run data found in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri. Make sure to have a volume called 001.mgz in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/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 endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed May 3 13:55:54 PDT 2006
Thanks, Darren
Darren L. Weber, Ph.D. Postdoctoral Scholar
Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA.
Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber
"To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org
iD8DBQFEWRnuxaCYN7qs0v4RAo91AKCisc5QNJhVDGySLbhZivaA/TBwjACeNuLs i71i+loDc67uAvWeHV37NzA= =eoyz -----END PGP SIGNATURE-----
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If you have only one acquisition and it is in mri/orig.mgz you can use the -nomotioncor flag to skip the motion correction step and carry on from there.
Jenni
On Wed, 3 May 2006, Darren Weber wrote:
--[PinePGP]--------------------------------------------------[begin]-- --[PinePGP]----------------------------------------------------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hi,
we have only 1 orig.mgz file, so motion correction is not required. In this case, it would be ideal if recon-all auto-detected or at least had an option to skip motion correction. As it is, it fails entirely when no 001.mgz file exists. I have a file called orig.mgz, should it be renamed to 001.mgz even though there is no 002.mgz?
endorphin.32> ls -l ucsf_disc01/mri/orig/ total 5784
- -rw-rw-rw- 1 dweber dnl 5907576 May 3 13:52 orig.mgz
endorphin.31> recon-all -subjid ucsf_disc01 -all INFO: SUBJECTS_DIR is /data/dnl-raid2/freesurfer/subjects Actual FREESURFER_HOME /data/dnl-raid1/freesurfer
- -rw-rw---- 1 dweber dnl 56553 May 3 13:55
/data/dnl-raid2/freesurfer/subjects/ucsf_disc01/scripts/recon-all.log Linux endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux WM removal version #-------------------------------------------- #@# MotionCor Wed May 3 13:55:54 PDT 2006 ERROR: no run data found in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/mri. Make sure to have a volume called 001.mgz in /data/dnl-raid2/freesurfer/subjects/ucsf_disc01/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 endorphin.ucsfmedicalcenter.org 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed May 3 13:55:54 PDT 2006
Thanks, Darren
Darren L. Weber, Ph.D. Postdoctoral Scholar
Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA.
Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber
"To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org
iD8DBQFEWRnuxaCYN7qs0v4RAo91AKCisc5QNJhVDGySLbhZivaA/TBwjACeNuLs i71i+loDc67uAvWeHV37NzA= =eoyz -----END PGP SIGNATURE-----
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
PinePGP: Encryption backend encountered error. --[PinePGP]----------------------------------------------------[end]--
freesurfer@nmr.mgh.harvard.edu
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Darren Weber -
Doug Greve -
Jenni Pacheco