Dear all,
trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell:
~>tcsh ~>source $FREESURFER_HOME/SetUpFreeSurfer.csh ~>setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~>cd $SUBJECTS_DIR ~>freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale
Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information.
1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64
Could anybody please telle me what's my problem?
Thanks Fabio
Are you running the dev version of freeview?
Ruopeng
On 06/19/2014 11:27 AM, Bernardoni, Fabio wrote:
Dear all,
trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell:
~>tcsh ~>source $FREESURFER_HOME/SetUpFreeSurfer.csh ~>setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~>cd $SUBJECTS_DIR ~>freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale
Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information.
1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64
Could anybody please telle me what's my problem?
Thanks Fabio
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Ruopeng,
I didn't install it myself, but I guess it is a stable one. Are you suggesting the timecourse option might simply not be available in the stable version?
thanks fabio
That is correct. timecourse option is only available in dev version. You can download it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
You may want to make a backup of your current freeview.bin file.
Ruopeng
On Jun 20, 2014, at 3:25 AM, Bernardoni, Fabio Fabio.Bernardoni@uniklinikum-dresden.de wrote:
Dear Ruopeng,
I didn't install it myself, but I guess it is a stable one. Are you suggesting the timecourse option might simply not be available in the stable version?
thanks fabio _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Fabio, I don't believe the 5.1 version of freeview had that flag. The tutorial instructions are written for 5.3 version of freeview. You can download a more recent version of freeview here (under Other Downloads & Info):
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
You may want to make a backup of your current freeview.bin file.
-Louis
On Thu, 19 Jun 2014, Bernardoni, Fabio wrote:
Dear all,
trying to follow the freesurfer longitudinal tutorial I encounter the following problem. Commands I digit in a new shell:
~>tcsh ~>source $FREESURFER_HOME/SetUpFreeSurfer.csh ~>setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/ ~>cd $SUBJECTS_DIR ~>freeview -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale
Output: Option 'timecourse' not recognized. Run 'freeview -h' for more information.
1- If I remove the timecourse option together with another 3 the command executes correctly. 2- As output of the bugr command I get: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-64-generic x86_64
Could anybody please telle me what's my problem?
Thanks Fabio
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bernardoni, Fabio -
Louis Nicholas Vinke -
Ruopeng Wang