Dear Freesurfer experts,
I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I followed the commands in tutorial and got error message, listed as follows. (Nevertheless, FS can read in volume and surface from GUI.)
Another question is, which one of Centos4 or Centos6 is more suitable for Ubuntu 13.04?
1. tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl
2. tkmedit -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz
Couldn't create output file .xdebug_tkmeditmghRead(/usr/local/freesurfer/subjects/bert/mri/mri/aseg.mgz, -1): could not open file
a window pop up: Error: loading segmentation mri/aseg.mgz Couldn't import the segmentation volume. Tkmedit couldn't read the segmentation specified. This could be because the segmentation volume wasn't a valid COR volume directory.
(Note: In fact, I can load segmentation volume from window.)
3. tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert
Thanks for your help, JoJo
JoJo,
I have not tried to recreate your issues on machine running Ubuntu 13.04 but have tried to run the commands on Ubuntu 12.04. To summarize:
1) Regarding your first issue... this is standard output to the terminal on certain OS's including Ubuntu. I got it when I tested your command but the tkmedit window still appeared. You may have to press enter after receiving the "Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl" but this is a normal warning message.
2) Change your command to the following: tkmedit -segmentation $SUBJECTS_DIR/bert/mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz
3) Again, I get the same warning, but the window still appears. Try hitting enter after you get the warning message.
-Zeke
On 08/23/2013 11:05 PM, JoJo wrote:
Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I followed the commands in tutorial and got error message, listed as follows. (Nevertheless, FS can read in volume and surface from GUI.) Another question is, which one of Centos4 or Centos6 is more suitable for Ubuntu 13.04?
- tkmedit bert orig.mgz
Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl 2. tkmedit -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz Couldn't create output file .xdebug_tkmeditmghRead(/usr/local/freesurfer/subjects/bert/mri/mri/aseg.mgz, -1): could not open file a window pop up: Error: loading segmentation mri/aseg.mgz Couldn't import the segmentation volume. Tkmedit couldn't read the segmentation specified. This could be because the segmentation volume wasn't a valid COR volume directory. (Note: In fact, I can load segmentation volume from window.) 3. tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert
Thanks for your help, JoJo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I had a similar error when using CentOS on VirtualBox. The error came from an error in the OpenCL driver. Are you running a virtualmachine? If not i would advise trying a different graphics driver. As to the CentOS/Ubuntu choice. I would go with CentOS as it seems more stable/constant and is more easy to also install FSL.
Best regards Rune Frandsen MD Danish Center for Sleep Medicine.
On Wed, Aug 28, 2013 at 5:18 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
JoJo,
I have not tried to recreate your issues on machine running Ubuntu 13.04 but have tried to run the commands on Ubuntu 12.04. To summarize:
- Regarding your first issue... this is standard output to the terminal
on certain OS's including Ubuntu. I got it when I tested your command but the tkmedit window still appeared. You may have to press enter after receiving the "Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl" but this is a normal warning message.
- Change your command to the following:
tkmedit -segmentation $SUBJECTS_DIR/bert/mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz
- Again, I get the same warning, but the window still appears. Try
hitting enter after you get the warning message.
-Zeke
On 08/23/2013 11:05 PM, JoJo wrote:
Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I followed the commands in tutorial and got error message, listed as follows. (Nevertheless, FS can read in volume and surface from GUI.) Another question is, which one of Centos4 or Centos6 is more suitable for Ubuntu 13.04?
- tkmedit bert orig.mgz
Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl 2. tkmedit -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz Couldn't create output file
.xdebug_tkmeditmghRead(/usr/local/freesurfer/subjects/bert/mri/mri/aseg.mgz,
-1): could not open file a window pop up: Error: loading segmentation mri/aseg.mgz Couldn't import the segmentation volume. Tkmedit couldn't read the segmentation specified. This could be because the segmentation volume wasn't a valid COR volume directory. (Note: In fact, I can load segmentation volume from window.) 3. tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert
Thanks for your help, JoJo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
JoJo -
Rune Frandsen -
Z K