Hi,
what happens if you open a terminal and type (without the double quotes): "which tkmedit" "which tkmedit.bin" If your path is set correctly there will something along the lines of (example from my mac):
hms-beagle:netperf-wrapper moeller$ which tkmedit /opt/freesurfer-Darwin-lion-stable-pub-v5.3.0/bin/tkmedit hms-beagle:netperf-wrapper moeller$ which tkmedit.bin /opt/freesurfer-Darwin-lion-stable-pub-v5.3.0/tktools/tkmedit.bin
Also please post the results of: "echo $PATH"
(This needs to contain /usr/local/freesurfer/tktools/ )
On Feb 4, 2014, at 14:30 , Saurabh Thakur srbhthkr@gmail.com wrote:
Hi,
I have got all the files necessary.
as per your instructions.
as well as environment is also set.
//===================================================================// freesurfer-Linux-centos4-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/saurabh/Desktop/saurabh_freesurfer MNI_DIR /usr/local/freesurfer/mni saurabh@saurabh-Dell-System-XPS-L502X:~$ 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 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:~$ tkedit subject1 orig.mgz tkedit: command not found
Okay, probably just a typo but it is called: TKMEDIT, not tkedit, note the missing M? So what is the output of
cd ${SUBJECTS_DIR}/ ; ls -all ; cd subject1/mri ; ls -all ; tkmedit -f rawavg.mgz
Best Regards sebastian
saurabh@saurabh-Dell-System-XPS-L502X:~$ //==========================================================//
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 6:11 PM, Markus Gschwind markus.gschwind@gmail.com wrote: Hi Saurabh,
Did you download the file again? You also can download old versions here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ so we are sure that there is not anything missing in your freesurfer folder. Can you write into the terminal: ls -l /usr/local/freesurfer
For your info: I get this:
~$ ls -l /usr/local/freesurfer total 372 -rw-r--r-- 1 root root 3302 May 14 2013 ASegStatsLUT.txt -rw-r--r-- 1 root root 728 May 14 2013 AUTHORS drwxr-xr-x 7 root root 4096 May 14 2013 average drwxr-xr-x 2 root root 32768 May 14 2013 bin -rw-r--r-- 1 root root 50 May 14 2013 build-stamp.txt drwxr-xr-x 3 root root 4096 May 14 2013 data -rw-r--r-- 1 root root 47514 May 14 2013 DefectLUT.txt drwxr-xr-x 3 root root 4096 May 14 2013 diffusion drwxr-xr-x 3 root root 4096 May 14 2013 docs -rw-r--r-- 1 root root 84833 May 14 2013 FreeSurferColorLUT.txt -rwxr-xr-x 1 root root 16760 May 14 2013 FreeSurferEnv.csh -rwxr-xr-x 1 root root 16846 May 14 2013 FreeSurferEnv.sh drwxr-xr-x 2 root root 4096 May 14 2013 fsafd drwxr-xr-x 5 root root 4096 May 14 2013 fsfast drwxr-xr-x 12 root root 4096 May 14 2013 lib -rw-r--r-- 1 root root 10297 May 14 2013 LICENSE drwxr-xr-x 3 root root 4096 May 14 2013 matlab drwxr-xr-x 9 root root 4096 Nov 1 2007 mni -rw-r--r-- 1 root root 4793 May 14 2013 NOTICE -rw-r--r-- 1 root root 635 May 14 2013 README -rw-r--r-- 1 root root 28445 May 14 2013 SegmentNoLUT.txt drwxr-xr-x 2 root root 4096 May 14 2013 sessions -rwxr-xr-x 1 root root 1352 May 14 2013 SetUpFreeSurfer.csh -rwxr-xr-x 1 root root 1342 May 14 2013 SetUpFreeSurfer.sh -rw-r--r-- 1 root root 4104 May 14 2013 Simple_surface_labels2009.txt drwxr-xr-x 15 root root 4096 Jan 28 16:24 subjects -rw-r--r-- 1 root root 1681 May 14 2013 tkmeditParcColorsCMA drwxr-xr-x 2 root root 4096 May 14 2013 tktools drwxr-xr-x 35 root root 4096 May 14 2013 trctrain -rw-r--r-- 1 root root 52 May 14 2013 VERSION -rw-r--r-- 1 root root 25944 May 14 2013 WMParcStatsLUT.txt
As you see there is also tktools.
What does it say if you type: ls -l /usr/local/freesurfer/tktools/
This is my version:
~$ ls -l /usr/local/freesurfer/tktools/ total 93888 -rwxr-xr-x 1 root root 46572 May 14 2013 fsgdfPlot.tcl -rw-r--r-- 1 root root 6180 May 14 2013 license.cortechs.txt -rwxr-xr-x 1 root root 17992 May 14 2013 tkanalyse.tcl -rwxr-xr-x 1 root root 722 May 14 2013 tkm_common.tcl -rwxr-xr-x 1 root root 1591 May 14 2013 tkm_dialog.tcl -rwxr-xr-x 1 root root 102 May 14 2013 tkmedit -rwxr-xr-x 1 root root 25409422 May 14 2013 tkmedit.bin -rwxr-xr-x 1 root root 154763 May 14 2013 tkmedit.tcl -rwxr-xr-x 1 root root 40941 May 14 2013 tkm_functional.tcl -rwxr-xr-x 1 root root 2805 May 14 2013 tkm_graph.tcl -rwxr-xr-x 1 root root 47324 May 14 2013 tkm_wrappers.tcl -rwxr-xr-x 1 root root 106 May 14 2013 tkregister -rwxr-xr-x 1 root root 106 May 14 2013 tkregister2 -rwxr-xr-x 1 root root 22267238 May 14 2013 tkregister2.bin -rwxr-xr-x 1 root root 22105890 May 14 2013 tkregister2_cmdl -rwxr-xr-x 1 root root 27967 May 14 2013 tkregister2.tcl -rwxr-xr-x 1 root root 27967 May 14 2013 tkregister.tcl -rwxr-xr-x 1 root root 103 May 14 2013 tksurfer -rwxr-xr-x 1 root root 25685088 May 14 2013 tksurfer.bin -rwxr-xr-x 1 root root 200280 May 14 2013 tksurfer.tcl -rwxr-xr-x 1 root root 56875 May 14 2013 tkUtils.tcl
Hope this helps, M
2014-02-04 Saurabh Thakur srbhthkr@gmail.com:
Hi,
I am using laptop with 8Gb RAM, i7 Core processor, and enough HDD....
still i m getting same erro ( /usr/local/freesurfer/tktools/tkmedit.bin: Command not found. ) because i m working on laptop...?
or
"recon-all --help " is working but tkmedit is not working
Hope to get response asap.
Thanks in advance.
Saurabh Thakur,
On Tue, Feb 4, 2014 at 2:09 PM, Markus Gschwind markus.gschwind@gmail.com wrote: Hi Saurabh,
I recently installed FS un ubuntu 12.04, and it was not difficult.
I would recommend that you again download the file from here http://surfer.nmr.mgh.harvard.edu/fswiki/Download (I took the Centos4 file)
to make sure that it is complete.
Than you "untar" the file at any given place (most people recomment /usr/local/ but you need to do it in "sudo" mode).
Then make sure that you put the license file at the right place (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall)
and adapt the configuration file (http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration)
I used bash and it worked well.
Take care that you have writing permission on the folders you want to use ($SUBJECT_DIR). For that reason I copied the folder "bert" to my home folder in order to be able to run the installation test as recommended here: http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
Hope that helps! Cheers, Markus
2014-02-04 Saurabh Thakur srbhthkr@gmail.com: Hello everyone,
Can u anyone help me in simplest and best way to install freesurfer on
i m not able to run command :
- tkmedit
- tksurfer.
System specification:
Dell laptop Ubuntu 12.04 LTS RAM 8Gb Graphics cards: Nvidia cards 1 Gb
Thanks in advance.
Saurabh Thakur,
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