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
saurabh@saurabh-Dell-System-XPS-L502X:~$ //==========================================================//
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 6:11 PM, Markus Gschwind markus.gschwind@gmail.comwrote:
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 ($SUBJECT_DIR). For that reason I copied the folder "bert" to my home folder in order to be able to run the installation test as recommended here: http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
Hope that helps! Cheers, Markus
2014-02-04 Saurabh Thakur srbhthkr@gmail.com:
Hello everyone,
Can u anyone help me in simplest and best way to install freesurfer on
*i m not able to run command : *
*1. tkmedit 2. tksurfer.System specification: *
Dell laptop Ubuntu 12.04 LTS RAM 8Gb Graphics cards: Nvidia cards 1 Gb
Thanks in advance.
Saurabh Thakur,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
what happens if you open a terminal and type (without the double quotes): "which tkmedit" "which tkmedit.bin" If your path is set correctly there will something along the lines of (example from my mac):
hms-beagle:netperf-wrapper moeller$ 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 ($SUBJECT_DIR). For that reason I copied the folder "bert" to my home folder in order to be able to run the installation test as recommended here: http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
Hope that helps! Cheers, Markus
2014-02-04 Saurabh Thakur srbhthkr@gmail.com: Hello everyone,
Can u anyone help me in simplest and best way to install freesurfer on
i m not able to run command :
- tkmedit
- tksurfer.
System specification:
Dell laptop Ubuntu 12.04 LTS RAM 8Gb Graphics cards: Nvidia cards 1 Gb
Thanks in advance.
Saurabh Thakur,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
On Tue, Feb 4, 2014 at 7:15 PM, Sebastian Moeller < sebastian.moeller1@rwth-aachen.de> wrote:
tkmedit -f rawavg.mgz
Hi Sebastian,
//================================================================// saurabh@saurabh-Dell-System-XPS-L502X:~$ which tkmedit /usr/local/freesurfer/bin/tkmedit saurabh@saurabh-Dell-System-XPS-L502X:~$ which tkmedit.bin /usr/local/freesurfer/tktools/tkmedit.bin saurabh@saurabh-Dell-System-XPS-L502X:~$ echo $PATH /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin: /usr/local/freesurfer/tktools :/usr/local/freesurfer/mni/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games saurabh@saurabh-Dell-System-XPS-L502X:~$
saurabh@saurabh-Dell-System-XPS-L502X:~$ cd $FREESURFER_HOME saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd subject1/mri bash: cd: subject1/mri: No such file or directory saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ ls -all total 392 drwxr-xr-x 16 root root 4096 Feb 4 16:17 . drwxr-xr-x 12 root root 4096 Feb 4 15:48 .. -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 40 Feb 4 16:17 .license -rw-r--r-- 1 root root 39 Feb 4 15:51 .license~ -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:/usr/local/freesurfer$ cd subject1/mri bash: cd: subject1/mri: No such file or directory saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit -f rawavg.mgz /usr/local/freesurfer/tktools/tkmedit.bin: Command not found. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
//===================================================================//
I m working on laptop where as in other desktop in our lab its working fine.
What should be the problem...?
cheers Saurabh Thakur
Hi again,
On Feb 4, 2014, at 14:57 , Saurabh Thakur srbhthkr@gmail.com wrote:
On Tue, Feb 4, 2014 at 7:15 PM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: tkmedit -f rawavg.mgz
Hi Sebastian,
//================================================================// saurabh@saurabh-Dell-System-XPS-L502X:~$ which tkmedit /usr/local/freesurfer/bin/tkmedit saurabh@saurabh-Dell-System-XPS-L502X:~$ which tkmedit.bin /usr/local/freesurfer/tktools/tkmedit.bin saurabh@saurabh-Dell-System-XPS-L502X:~$ echo $PATH /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games saurabh@saurabh-Dell-System-XPS-L502X:~$
Good, so the path is set up correctly (as expected otherwise the freesurfer setup script would have complained)
saurabh@saurabh-Dell-System-XPS-L502X:~$ cd $FREESURFER_HOME
Nah, cd ${SUBJECTS_DIR} not ${FREESURFER_HOME} we want a look at the data directories, not the freesurfer distribution (but that does not matter much see later).
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd subject1/mri bash: cd: subject1/mri: No such file or directory saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ ls -all total 392 drwxr-xr-x 16 root root 4096 Feb 4 16:17 . drwxr-xr-x 12 root root 4096 Feb 4 15:48 .. -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 40 Feb 4 16:17 .license -rw-r--r-- 1 root root 39 Feb 4 15:51 .license~ -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:/usr/local/freesurfer$ cd subject1/mri bash: cd: subject1/mri: No such file or directory saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit -f rawavg.mgz /usr/local/freesurfer/tktools/tkmedit.bin: Command not found.
could you post the output of: "cat `which tkmedit`" Note the ` back ticks around the which tkmedit please? Mine looks like: hms-beagle:KOFIKO moeller$ cat `which tkmedit` #!/bin/tcsh -ef source $FREESURFER_HOME/bin/tcl_setup exec $FREESURFER_HOME/tktools/tkmedit.bin $argv hms-beagle:KOFIKO moeller$
I could imagine that somehow the invoked tcsh instance does not have the correct path available. To test this hypothesis could you save the following to your home directory as tkmedit2
#!/bin/tcsh -Fe source $FREESURFER_HOME/bin/tcl_setup echo ${PATH} exec $FREESURFER_HOME/tktools/tkmedit.bin $argv
and test: tkmedit subject1 rawavg.mgz (and post the output)
best regards Sebastian
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
//===================================================================//
I m working on laptop where as in other desktop in our lab its working fine.
What should be the problem...?
cheers Saurabh Thakur
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller < sebastian.moeller1@rwth-aachen.de> wrote:
tkmedit subject1 rawavg.mgz
Hi Sebastian,
tkmedit is properly get attached. tat means tcsh is working properly. //==========================================================// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd $SUBJECTS_DIR saurabh@saurabh-Dell-System-XPS-L502X:~/Desktop/saurabh_freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cat `which tkmedit` #!/bin/tcsh -ef source $FREESURFER_HOME/bin/tcl_setup exec $FREESURFER_HOME/tktools/tkmedit.bin $argv saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit subject1 rawavg.mgz /usr/local/freesurfer/tktools/tkmedit.bin: Command not found. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ //===============================================================//
Still error is present...?
cheers Saurabh Thakur,
Hi,
On Feb 4, 2014, at 15:38 , Saurabh Thakur srbhthkr@gmail.com wrote:
On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: tkmedit subject1 rawavg.mgz
Hi Sebastian,
tkmedit is properly get attached. tat means tcsh is working properly. //==========================================================// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd $SUBJECTS_DIR saurabh@saurabh-Dell-System-XPS-L502X:~/Desktop/saurabh_freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cat `which tkmedit` #!/bin/tcsh -ef source $FREESURFER_HOME/bin/tcl_setup exec $FREESURFER_HOME/tktools/tkmedit.bin $argv saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit subject1 rawavg.mgz /usr/local/freesurfer/tktools/tkmedit.bin: Command not found. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ //===============================================================//
Still error is present…?
Looks like it, so let me propose: I could imagine that somehow the invoked tcsh instance does not have the correct path available. To test this hypothesis could you save the following to your home directory as tkmedit2 So in other words, open your preferred editor (edit?) create a new file with the name tkmedit2 in your home directory, and copy and paste the following into it and save it again:
#!/bin/tcsh -Fe source $FREESURFER_HOME/bin/tcl_setup echo ${PATH} exec $FREESURFER_HOME/tktools/tkmedit.bin $argv exit 0 #last line…
and test: tkmedit2 subject1 rawavg.mgz (and post the output) in my last mail there was a typo here, the goal is to call the just created tkmedit2 and see whether the $PATCH contains the tktools directory.
best regards Sebastian
cheers Saurabh Thakur,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Sebastian,
I have copied in same tktools and tried to run the *tkmedit2 subject1 rawavg.mgz*
got the output:
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ *tkmedit2 subject1 rawavg.mgz* bash: /usr/local/freesurfer/tktools/tkmedit2: Permission denied saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$* sudo tkmedit2 subject1 rawavg.mgz* sudo: tkmedit2: command not found saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$
Am i doing it right...?
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller < sebastian.moeller1@rwth-aachen.de> wrote:
Hi,
On Feb 4, 2014, at 15:38 , Saurabh Thakur srbhthkr@gmail.com wrote:
On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller <
sebastian.moeller1@rwth-aachen.de> wrote:
tkmedit subject1 rawavg.mgz
Hi Sebastian,
tkmedit is properly get attached. tat means tcsh is working properly. //==========================================================// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd
$SUBJECTS_DIR
saurabh@saurabh-Dell-System-XPS-L502X:~/Desktop/saurabh_freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cat `which
tkmedit`
#!/bin/tcsh -ef source $FREESURFER_HOME/bin/tcl_setup exec $FREESURFER_HOME/tktools/tkmedit.bin $argv saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit
subject1 rawavg.mgz
/usr/local/freesurfer/tktools/tkmedit.bin: Command not found. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ //===============================================================//
Still error is present...?
Looks like it, so let me propose: I could imagine that somehow the invoked tcsh instance does not have the correct path available. To test this hypothesis could you save the following to your home directory as tkmedit2 So in other words, open your preferred editor (edit?) create a new file with the name tkmedit2 in your home directory, and copy and paste the following into it and save it again:
#!/bin/tcsh -Fe source $FREESURFER_HOME/bin/tcl_setup echo ${PATH} exec $FREESURFER_HOME/tktools/tkmedit.bin $argv exit 0 #last line...
and test: tkmedit2 subject1 rawavg.mgz (and post the output) in my last mail there was a typo here, the goal is to call the just created tkmedit2 and see whether the $PATCH contains the tktools directory.
best regards Sebastian
cheers Saurabh Thakur,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
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Hi Saurabh,
On Feb 4, 2014, at 16:18 , Saurabh Thakur srbhthkr@gmail.com wrote:
Hi Sebastian,
I have copied in same tktools and tried to run the tkmedit2 subject1 rawavg.mgz
got the output:
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ tkmedit2 subject1 rawavg.mgz bash: /usr/local/freesurfer/tktools/tkmedit2: Permission denied saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ sudo tkmedit2 subject1 rawavg.mgz sudo: tkmedit2: command not found saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$
Am i doing it right…?
Oh, I guess tkmedit2 is not executable, so please run (from a shell in the directory where tkmedit2 is located): chmod u+x tkmedit2 and try to run it again from the directory where it is located: "./tkmedit2 subject1 rawavg.mgz"
best regards Sebastian
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: Hi,
On Feb 4, 2014, at 15:38 , Saurabh Thakur srbhthkr@gmail.com wrote:
On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: tkmedit subject1 rawavg.mgz
Hi Sebastian,
tkmedit is properly get attached. tat means tcsh is working properly. //==========================================================// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd $SUBJECTS_DIR saurabh@saurabh-Dell-System-XPS-L502X:~/Desktop/saurabh_freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cat `which tkmedit` #!/bin/tcsh -ef source $FREESURFER_HOME/bin/tcl_setup exec $FREESURFER_HOME/tktools/tkmedit.bin $argv saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit subject1 rawavg.mgz /usr/local/freesurfer/tktools/tkmedit.bin: Command not found. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ //===============================================================//
Still error is present…?
Looks like it, so let me propose: I could imagine that somehow the invoked tcsh instance does not have the correct path available. To test this hypothesis could you save the following to your home directory as tkmedit2 So in other words, open your preferred editor (edit?) create a new file with the name tkmedit2 in your home directory, and copy and paste the following into it and save it again:
#!/bin/tcsh -Fe source $FREESURFER_HOME/bin/tcl_setup echo ${PATH} exec $FREESURFER_HOME/tktools/tkmedit.bin $argv exit 0 #last line…
and test: tkmedit2 subject1 rawavg.mgz (and post the output) in my last mail there was a typo here, the goal is to call the just created tkmedit2 and see whether the $PATCH contains the tktools directory.
best regards Sebastian
cheers Saurabh Thakur,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Sebastian ,Bruce and Markus.
I got the freesurfer running using
freesurfer-x86_64-unknown-linux-gnu-stable5-20130513
Thanks for all your help.
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 9:18 PM, Sebastian Moeller < sebastian.moeller1@rwth-aachen.de> wrote:
Hi Saurabh,
On Feb 4, 2014, at 16:18 , Saurabh Thakur srbhthkr@gmail.com wrote:
Hi Sebastian,
I have copied in same tktools and tried to run the tkmedit2 subject1
rawavg.mgz
got the output:
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$
tkmedit2 subject1 rawavg.mgz
bash: /usr/local/freesurfer/tktools/tkmedit2: Permission denied saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$
sudo tkmedit2 subject1 rawavg.mgz
sudo: tkmedit2: command not found saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$
Am i doing it right...?
Oh, I guess tkmedit2 is not executable, so please run (from ashell in the directory where tkmedit2 is located): chmod u+x tkmedit2 and try to run it again from the directory where it is located: "./tkmedit2 subject1 rawavg.mgz"
best regards Sebastian
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller <
sebastian.moeller1@rwth-aachen.de> wrote:
Hi,
On Feb 4, 2014, at 15:38 , Saurabh Thakur srbhthkr@gmail.com wrote:
On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller <
sebastian.moeller1@rwth-aachen.de> wrote:
tkmedit subject1 rawavg.mgz
Hi Sebastian,
tkmedit is properly get attached. tat means tcsh is working properly. //==========================================================// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd
$SUBJECTS_DIR
saurabh@saurabh-Dell-System-XPS-L502X:~/Desktop/saurabh_freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cat
`which tkmedit`
#!/bin/tcsh -ef source $FREESURFER_HOME/bin/tcl_setup exec $FREESURFER_HOME/tktools/tkmedit.bin $argv saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit
subject1 rawavg.mgz
/usr/local/freesurfer/tktools/tkmedit.bin: Command not found. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ //===============================================================//
Still error is present...?
Looks like it, so let me propose: I could imagine that somehow the invoked tcsh instance does not have the
correct path available. To test this hypothesis could you save the following to your home directory as tkmedit2
So in other words, open your preferred editor (edit?) create anew file with the name tkmedit2 in your home directory, and copy and paste the following into it and save it again:
#!/bin/tcsh -Fe source $FREESURFER_HOME/bin/tcl_setup echo ${PATH} exec $FREESURFER_HOME/tktools/tkmedit.bin $argv exit 0 #last line...
and test: tkmedit2 subject1 rawavg.mgz (and post the output) in my last mail there was a typo here, the goal is
to call the just created tkmedit2 and see whether the $PATCH contains the tktools directory.
best regards Sebastian
cheers Saurabh Thakur,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
glad to hear it worked out Bruce On Wed, 5 Feb 2014, Saurabh Thakur wrote:
Hi Sebastian ,Bruce and Markus.
I got the freesurfer running using
freesurfer-x86_64-unknown-linux-gnu-stable5-20130513
Thanks for all your help.
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 9:18 PM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: Hi Saurabh,
On Feb 4, 2014, at 16:18 , Saurabh Thakur <srbhthkr@gmail.com> wrote: > Hi Sebastian, > > I have copied in same tktools and tried to run the tkmedit2 subject1 rawavg.mgz > > got the output: > > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ tkmedit2 subject1 rawavg.mgz > bash: /usr/local/freesurfer/tktools/tkmedit2: Permission denied > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ sudo tkmedit2 subject1 rawavg.mgz > sudo: tkmedit2: command not found > saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ >Am i doing it right…?
Oh, I guess tkmedit2 is not executable, so please run (from a shell in the directory where tkmedit2 is located): chmod u+x tkmedit2 and try to run it again from the directory where it is located: "./tkmedit2 subject1 rawavg.mgz"
best regards Sebastian
cheers Saurabh Thakur,
On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller
sebastian.moeller1@rwth-aachen.de wrote:
Hi,
On Feb 4, 2014, at 15:38 , Saurabh Thakur srbhthkr@gmail.com
wrote:
On Tue, Feb 4, 2014 at 7:41 PM, Sebastian Moeller
sebastian.moeller1@rwth-aachen.de wrote:
tkmedit subject1 rawavg.mgz
Hi Sebastian,
tkmedit is properly get attached. tat means tcsh is working properly. //==========================================================// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cd
$SUBJECTS_DIR
saurabh@saurabh-Dell-System-XPS-L502X:~/Desktop/saurabh_freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ cat
`which tkmedit`
#!/bin/tcsh -ef source $FREESURFER_HOME/bin/tcl_setup exec $FREESURFER_HOME/tktools/tkmedit.bin $argv saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
tkmedit subject1 rawavg.mgz
/usr/local/freesurfer/tktools/tkmedit.bin: Command not found. saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$
//===============================================================//
Still error is present…?
Looks like it, so let me propose: I could imagine that somehow the invoked tcsh instance does not have
the correct path available. To test this hypothesis could you save the following to your home directory as tkmedit2
So in other words, open your preferred editor (edit?) create
a new file with the name tkmedit2 in your home directory, and copy and paste the following into it and save it again:
#!/bin/tcsh -Fe source $FREESURFER_HOME/bin/tcl_setup echo ${PATH} exec $FREESURFER_HOME/tktools/tkmedit.bin $argv exit 0 #last line…
and test: tkmedit2 subject1 rawavg.mgz (and post the output) in my last mail there was a typo here, the
goal is to call the just created tkmedit2 and see whether the $PATCH contains the tktools directory.
best regards Sebastian
cheers Saurabh Thakur,
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Bruce Fischl -
Saurabh Thakur -
Sebastian Moeller