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 <[email protected]>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 <[email protected]>: > > 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 < >> [email protected]> 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 <[email protected]>: >>> >>>> 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 >>>> [email protected] >>>> 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. >>>> >>>> >>> >> >
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