yes, particularly since 5.2 was deprecated. Thanks for pointing this out Sebastian

Bruce

On Tue, 4 Feb 2014, Sebastian Moeller wrote:

Hi again,

On Feb 4, 2014, at 14:44 , Saurabh Thakur <srbhthkr@gmail.com> wrote:

On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
ls -l  /usr/local/freesurfer/tktools

Hi Bruce,

I m sending you some result :

//==========================================================///
freesurfer-Linux-centos4-stable-pub-v5.2.0 --------

        It might make sense to switch to freesurfer 5.3 since you have not yet produced any surfaces yet, so switching will have no legacy costs.

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/saurabh/Desktop/saurabh_freesurfer
MNI_DIR           /usr/local/freesurfer/mni

saurabh@saurabh-Dell-System-XPS-L502X:~$ ls -l /usr/local/freesurfer
total 376
-rw-r--r--  1 root root  3302 Mar  1  2013 ASegStatsLUT.txt
-rw-r--r--  1 root root   728 Mar  1  2013 AUTHORS
drwxr-xr-x  7 root root  4096 Mar  1  2013 average
drwxr-xr-x  2 root root 36864 Mar  1  2013 bin
-rw-r--r--  1 root root    43 Mar  1  2013 build-stamp.txt
drwxr-xr-x  3 root root  4096 Mar  1  2013 data
-rw-r--r--  1 root root 47514 Mar  1  2013 DefectLUT.txt
drwxr-xr-x  3 root root  4096 Mar  1  2013 diffusion
drwxr-xr-x  3 root root  4096 Mar  1  2013 docs
-rw-r--r--  1 root root 84833 Mar  1  2013 FreeSurferColorLUT.txt
-rwxr-xr-x  1 root root 16760 Mar  1  2013 FreeSurferEnv.csh
-rwxr-xr-x  1 root root 16846 Mar  1  2013 FreeSurferEnv.sh
drwxr-xr-x  2 root root  4096 Mar  1  2013 fsafd
drwxr-xr-x  5 root root  4096 Mar  1  2013 fsfast
drwxr-xr-x 12 root root  4096 Mar  1  2013 lib
-rw-r--r--  1 root root 10297 Mar  1  2013 LICENSE
drwxr-xr-x  3 root root  4096 Mar  1  2013 matlab
drwxr-xr-x  8 root root  4096 Feb 21  2010 mni
-rw-r--r--  1 root root  4793 Mar  1  2013 NOTICE
-rw-r--r--  1 root root   635 Mar  1  2013 README
-rw-r--r--  1 root root 28445 Mar  1  2013 SegmentNoLUT.txt
drwxr-xr-x  2 root root  4096 Mar  1  2013 sessions
-rwxr-xr-x  1 root root  1303 Mar  1  2013 SetUpFreeSurfer.csh
-rwxr-xr-x  1 root root  1293 Mar  1  2013 SetUpFreeSurfer.sh
-rw-r--r--  1 root root  4104 Mar  1  2013 Simple_surface_labels2009.txt
drwxr-xr-x 14 root root  4096 Mar  1  2013 subjects
-rw-r--r--  1 root root  1681 Mar  1  2013 tkmeditParcColorsCMA
drwxr-xr-x  2 root root  4096 Mar  1  2013 tktools
drwxr-xr-x 35 root root  4096 Mar  1  2013 trctrain
-rw-r--r--  1 root root    50 Mar  1  2013 VERSION
-rw-r--r--  1 root root 25944 Mar  1  2013 WMParcStatsLUT.txt

Result no.1

saurabh@saurabh-Dell-System-XPS-L502X:~$ ls -l  /usr/local/freesurfer/tktools
total 71772
-rwxr-xr-x 1 root root    46572 Mar  1  2013 fsgdfPlot.tcl
-rw-r--r-- 1 root root     6180 Mar  1  2013 license.cortechs.txt
-rwxr-xr-x 1 root root    17992 Mar  1  2013 tkanalyse.tcl
-rwxr-xr-x 1 root root      722 Mar  1  2013 tkm_common.tcl
-rwxr-xr-x 1 root root     1591 Mar  1  2013 tkm_dialog.tcl
-rwxr-xr-x 1 root root      102 Mar  1  2013 tkmedit
-rwxr-xr-x 1 root root 19541885 Feb  4 18:52 tkmedit.bin
-rwxr-xr-x 1 root root   154763 Mar  1  2013 tkmedit.tcl
-rwxr-xr-x 1 root root    40941 Mar  1  2013 tkm_functional.tcl
-rwxr-xr-x 1 root root     2805 Mar  1  2013 tkm_graph.tcl
-rwxr-xr-x 1 root root    47324 Mar  1  2013 tkm_wrappers.tcl
-rwxr-xr-x 1 root root      106 Mar  1  2013 tkregister
-rwxr-xr-x 1 root root      106 Mar  1  2013 tkregister2
-rwxr-xr-x 1 root root 16911243 Mar  1  2013 tkregister2.bin
-rwxr-xr-x 1 root root 16792599 Mar  1  2013 tkregister2_cmdl
-rwxr-xr-x 1 root root    27967 Mar  1  2013 tkregister2.tcl
-rwxr-xr-x 1 root root    27967 Mar  1  2013 tkregister.tcl
-rwxr-xr-x 1 root root      103 Mar  1  2013 tksurfer
-rwxr-xr-x 1 root root 19578559 Feb  4 18:52 tksurfer.bin
-rwxr-xr-x 1 root root   200280 Mar  1  2013 tksurfer.tcl
-rwxr-xr-x 1 root root    56875 Mar  1  2013 tkUtils.tcl
saurabh@saurabh-Dell-System-XPS-L502X:~$


Result 2:
tcsh is working

and updated
saurabh@saurabh-Dell-System-XPS-L502X:~$ tcsh
saurabh-Dell-System-XPS-L502X:~>

saurabh-Dell-System-XPS-L502X:~> echo $version
tcsh 6.17.06 (Astron) 2011-04-15 (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filed


Result 3:

I want to start tkmedit asap.

how can i start gui .....?


Solution for error i m looking for is:

saurabh@saurabh-Dell-System-XPS-L502X:~$ tkedit subject1 orig.mgz
tkedit: command not found

        Mmmh, if I may offer a guess:

tkmedit subject1 orig.mgz

might actually work (but I doubt that, as you had shown errors about tkmedit.bin earlier, and tkmedit calls tkmedit.bin in the end)


best regards
        Sebastian

//======================================================================//


cheers
Saurabh Thakur,


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