Ok, lots of problems! First, is the tktools directory empty? Run:
ls -l /usr/local/freesurfer/tktools
if there is nothing there, you will need to download and install them.
Second: you are getting the warning "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!". Can you ask your sysadmin to update your version of tcsh (or do it yourself)?
Third: one of your input volumes (or all of them) are invalid. Are you sure that they are anatomical T1-weighted acquisitions? The warning you are getting about multi-frame volumes might mean you have specified an fMRI dataset accidentally. Can you run:
mri_info /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/001.mgz mri_info /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/002.mgz mri_info /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/003.mgz
and send us the results?
cheers Bruce
On Tue, 4 Feb 2014, Saurabh Thakur wrote:
Hi Everyone,
Terminal output is: ///------------------------------------------------------------------------ ------------------------------////// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Command not found.
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tksurfer /usr/local/freesurfer/tktools/tksurfer.bin: Command not found.
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ recon-all
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
USAGE: recon-all
Required Arguments: -subjid <subjid> -<process directive>
Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all
Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial -hemi ?h : just do lh or rh (default is to do both) . . . . ///------------------------------------------------------------------------ --------------------------//
can any one help me in this problem.....?
Why tkmedit is not working.
I am seriously looking for solution asap.
Thanks in advance.
Saurabh