Hi again, you could try: wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz
which in theory is restartable and should resume a download if interrupted. Also I would like to recommend that you test whether your operating system is 64bit: "uname -a" if this contains the substring x86_64 somewhere (and not i386, i586 or i686) you should switch to: wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz Make sure the download has finished (all the data has transferred nd the size of the downloaded archive matches the size stated on: http://surfer.nmr.mgh.harvard.edu/fswiki/Download If the downloaded archive is too small just use the same wget command line again (and again until all the data is on your harddisk) Also check whether: "md5 freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz" returns: e0f1cb75818920ee441c2e162b94f21f freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz or "md5 freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz" 084d341cdf98305127aaeee48a6f4e0b freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0.tar.gz depending on which version you downloaded. That way you should have a know good installation archive. best Sebastian On Feb 4, 2014, at 15:14 , Saurabh Thakur <srbht...@gmail.com> wrote: > I have downloaded in morning only. > > But seems there is some problem while downloading. > > While unzipping it is saying : > > gzip: stdin: unexpected end of file > freesurfer/trctrain/trc007/dlabel/cvs/rh.ilf_AS_roi1.flt.nii.gz > tar: Unexpected EOF in archive > tar: Unexpected EOF in archive > tar: Error is not recoverable: exiting now > > In all i could extract about 256 packages: > > total 256 > > saurabh@saurabh-Dell-System-XPS-L502X:~/Downloads/freesurfer$ ls -all > total 256 > drwxr-xr-x 10 saurabh saurabh 4096 May 14 2013 . > drwxr-xr-x 3 saurabh saurabh 4096 Feb 4 19:36 .. > -rw-r--r-- 1 saurabh saurabh 728 May 14 2013 AUTHORS > drwxr-xr-x 2 saurabh saurabh 36864 May 14 2013 bin > -rw-r--r-- 1 saurabh saurabh 43 May 14 2013 build-stamp.txt > drwxr-xr-x 3 saurabh saurabh 4096 May 14 2013 data > -rw-r--r-- 1 saurabh saurabh 47514 May 14 2013 DefectLUT.txt > drwxr-xr-x 3 saurabh saurabh 4096 May 14 2013 docs > -rw-r--r-- 1 saurabh saurabh 84833 May 14 2013 FreeSurferColorLUT.txt > -rwxr-xr-x 1 saurabh saurabh 16760 May 14 2013 FreeSurferEnv.csh > drwxr-xr-x 12 saurabh saurabh 4096 May 14 2013 lib > drwxr-xr-x 8 saurabh saurabh 4096 Feb 21 2010 mni > -rw-r--r-- 1 saurabh saurabh 4793 May 14 2013 NOTICE > -rwxr-xr-x 1 saurabh saurabh 1303 May 14 2013 SetUpFreeSurfer.csh > -rw-r--r-- 1 saurabh saurabh 4104 May 14 2013 Simple_surface_labels2009.txt > drwxr-xr-x 14 saurabh saurabh 4096 May 14 2013 subjects > drwxr-xr-x 2 saurabh saurabh 4096 May 14 2013 tktools > drwxr-xr-x 32 saurabh saurabh 4096 May 14 2013 trctrain > -rw-r--r-- 1 saurabh saurabh 50 May 14 2013 VERSION > > saurabh@saurabh-Dell-System-XPS-L502X:~/Downloads/freesurfer$ gedit VERSION > saurabh@saurabh-Dell-System-XPS-L502X:~/Downloads/freesurfer$ > > freesurfer-i686-redhat-linux-gnu-stable5-20130513 > > I wil download it one more time. > > and get back to you. > > cheers > Saurabh Thakur, > > > > > > > On Tue, Feb 4, 2014 at 7:26 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > 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 <srbht...@gmail.com> wrote: > > > On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl <fis...@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, > > > _______________________________________________ > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
