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
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