Dear Freesurfer Users, during the creation of average brain with Freesurfer, I got the following ERROR message:
getpwdcmd: command not found ERROR: format for rh.orig.avg.area.mgh not recognized. ERROR: make_average_surface
do you have any idea what this might be? The Freesurfer version I'm using is 4.4.0. I also attach the log file. I would appreciate your help. Sincerely, Anna Rotarska-Jagiela
Try adding $FREESURFER_HOME/fsfast/bin to your path.
doug
Anna Rotarska-Jagiela wrote:
Dear Freesurfer Users, during the creation of average brain with Freesurfer, I got the following ERROR message:
getpwdcmd: command not found ERROR: format for rh.orig.avg.area.mgh not recognized. ERROR: make_average_surface
do you have any idea what this might be? The Freesurfer version I'm using is 4.4.0. I also attach the log file. I would appreciate your help. Sincerely, Anna Rotarska-Jagiela
--
Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska@mpih-frankfurt.mpg.de mailto:rotarska@mpih-frankfurt.mpg.de Phone: +49 69 6301 83782 Fax: +49 69 6301 3833
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug, thank you for your response. The path you named is added. Is there anything else we can check? Anna
2009/11/16 Douglas N Greve greve@nmr.mgh.harvard.edu
Try adding $FREESURFER_HOME/fsfast/bin to your path.
doug
Anna Rotarska-Jagiela wrote:
Dear Freesurfer Users, during the creation of average brain with Freesurfer, I got the following ERROR message:
getpwdcmd: command not found ERROR: format for rh.orig.avg.area.mgh not recognized. ERROR: make_average_surface
do you have any idea what this might be? The Freesurfer version I'm using is 4.4.0. I also attach the log file. I would appreciate your help. Sincerely, Anna Rotarska-Jagiela
--
Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska@mpih-frankfurt.mpg.de mailto:rotarska@mpih-frankfurt.mpg.de Phone: +49 69 6301 83782 Fax: +49 69 6301 3833
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What happens when you type
which getpwdcmd
And can you see the file in $FREESURFER_HOME/fsfast/bin?
Anna Rotarska-Jagiela wrote:
Dear Doug, thank you for your response. The path you named is added. Is there anything else we can check? Anna
2009/11/16 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Try adding $FREESURFER_HOME/fsfast/bin to your path. doug Anna Rotarska-Jagiela wrote: > > > Dear Freesurfer Users, > during the creation of average brain with Freesurfer, I got the > following ERROR message: > > > getpwdcmd: command not found > > > ERROR: format for rh.orig.avg.area.mgh not recognized. > > > ERROR: make_average_surface > > do you have any idea what this might be? The Freesurfer version I'm > using is 4.4.0. I also attach the log file. > I would appreciate your help. > Sincerely, > Anna Rotarska-Jagiela > > > > -- > ------ > Dr. Anna Rotarska-Jagiela > Max Planck Institute for Brain Research > Department of Neurophysiology > Deutschordenstr. 46 > 60528 Frankfurt a.M. > Germany > Email: rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de> > <mailto:rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de>> > Phone: +49 69 6301 83782 > Fax: +49 69 6301 3833 > ------ > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm > ------ > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--
Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska@mpih-frankfurt.mpg.de mailto:rotarska@mpih-frankfurt.mpg.de Phone: +49 69 6301 83782 Fax: +49 69 6301 3833
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
When I type which getpwdcmd, I get: /apps/prod/i686/freesurfer-4.4.0/fsfast/bin/getpwdcmd And I checked, the file is there.
Anna
2009/11/17 Douglas N Greve greve@nmr.mgh.harvard.edu
What happens when you type
which getpwdcmd
And can you see the file in $FREESURFER_HOME/fsfast/bin?
Anna Rotarska-Jagiela wrote:
Dear Doug, thank you for your response. The path you named is added. Is there anything else we can check? Anna
2009/11/16 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: greve@nmr.mgh.harvard.edu>
Try adding $FREESURFER_HOME/fsfast/bin to your path.
doug
Anna Rotarska-Jagiela wrote:
Dear Freesurfer Users, during the creation of average brain with Freesurfer, I got the following ERROR message:
getpwdcmd: command not found ERROR: format for rh.orig.avg.area.mgh not recognized. ERROR: make_average_surface
do you have any idea what this might be? The Freesurfer version I'm using is 4.4.0. I also attach the log file. I would appreciate your help. Sincerely, Anna Rotarska-Jagiela
--
Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska@mpih-frankfurt.mpg.de
mailto:rotarska@mpih-frankfurt.mpg.de
<mailto:rotarska@mpih-frankfurt.mpg.de
mailto:rotarska@mpih-frankfurt.mpg.de>
Phone: +49 69 6301 83782 Fax: +49 69 6301 3833
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska@mpih-frankfurt.mpg.de mailto: rotarska@mpih-frankfurt.mpg.de
Phone: +49 69 6301 83782 Fax: +49 69 6301 3833
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
And does the "getpwdcmd: command not found" still occur?
Anna Rotarska-Jagiela wrote:
When I type which getpwdcmd, I get: /apps/prod/i686/freesurfer-4.4.0/fsfast/bin/getpwdcmd And I checked, the file is there.
Anna
2009/11/17 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
What happens when you type which getpwdcmd And can you see the file in $FREESURFER_HOME/fsfast/bin? Anna Rotarska-Jagiela wrote: Dear Doug, thank you for your response. The path you named is added. Is there anything else we can check? Anna 2009/11/16 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Try adding $FREESURFER_HOME/fsfast/bin to your path. doug Anna Rotarska-Jagiela wrote: > > > Dear Freesurfer Users, > during the creation of average brain with Freesurfer, I got the > following ERROR message: > > > getpwdcmd: command not found > > > ERROR: format for rh.orig.avg.area.mgh not recognized. > > > ERROR: make_average_surface > > do you have any idea what this might be? The Freesurfer version I'm > using is 4.4.0. I also attach the log file. > I would appreciate your help. > Sincerely, > Anna Rotarska-Jagiela > > > > -- > ------ > Dr. Anna Rotarska-Jagiela > Max Planck Institute for Brain Research > Department of Neurophysiology > Deutschordenstr. 46 > 60528 Frankfurt a.M. > Germany > Email: rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de> <mailto:rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de>> > <mailto:rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de> <mailto:rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de>>> > Phone: +49 69 6301 83782 > Fax: +49 69 6301 3833 > ------ > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm > ------ > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ------ Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de> <mailto:rotarska@mpih-frankfurt.mpg.de <mailto:rotarska@mpih-frankfurt.mpg.de>> Phone: +49 69 6301 83782 Fax: +49 69 6301 3833 ------ http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm ------ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>--
Dr. Anna Rotarska-Jagiela Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt a.M. Germany Email: rotarska@mpih-frankfurt.mpg.de mailto:rotarska@mpih-frankfurt.mpg.de Phone: +49 69 6301 83782 Fax: +49 69 6301 3833
http://www.mpih-frankfurt.mpg.de/global/Np/Staff/rotarska.htm
freesurfer@nmr.mgh.harvard.edu
-
Anna Rotarska-Jagiela -
Douglas N Greve