Hi Everyone,
Terminal output is: ///------------------------------------------------------------------------------------------------------////// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$* tkmedit* /usr/local/freesurfer/tktools*/tkmedit.bin: Command not found.*
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ *tksurfer* /usr/local/freesurfer/tktools*/tksurfer.bin: Command not found*.
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ *recon-all*
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
USAGE: recon-all
Required Arguments: -subjid <subjid> -<process directive>
Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all
Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial -hemi ?h : just do lh or rh (default is to do both) . . . . ///--------------------------------------------------------------------------------------------------//
can any one help me in this problem.....?
Why* tkmedit *is not working.
I am seriously looking for solution asap.
Thanks in advance.
*Saurabh *
Ok, lots of problems! First, is the tktools directory empty? Run:
ls -l /usr/local/freesurfer/tktools
if there is nothing there, you will need to download and install them.
Second: you are getting the warning "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!". Can you ask your sysadmin to update your version of tcsh (or do it yourself)?
Third: one of your input volumes (or all of them) are invalid. Are you sure that they are anatomical T1-weighted acquisitions? The warning you are getting about multi-frame volumes might mean you have specified an fMRI dataset accidentally. Can you run:
mri_info /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/001.mgz mri_info /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/002.mgz mri_info /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/003.mgz
and send us the results?
cheers Bruce
On Tue, 4 Feb 2014, Saurabh Thakur wrote:
Hi Everyone,
Terminal output is: ///------------------------------------------------------------------------ ------------------------------////// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Command not found.
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tksurfer /usr/local/freesurfer/tktools/tksurfer.bin: Command not found.
saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ recon-all
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
USAGE: recon-all
Required Arguments: -subjid <subjid> -<process directive>
Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all
Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial -hemi ?h : just do lh or rh (default is to do both) . . . . ///------------------------------------------------------------------------ --------------------------//
can any one help me in this problem.....?
Why tkmedit is not working.
I am seriously looking for solution asap.
Thanks in advance.
Saurabh
On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
ls -l /usr/local/freesurfer/tktools
Hi Bruce,
I m sending you some result :
//==========================================================///
*freesurfer-Linux-centos4-stable-pub-v5.2.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurferFSFAST_HOME /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /home/saurabh/Desktop/saurabh_freesurferMNI_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 roo*t 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 $version *tcsh 6.17.06 (Astron)* 2011-04-15 (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec
Result 3:
I want to start* tkmedit* asap.
how can i start gui .....?
Solution for error i m looking for is:
saurabh@saurabh-Dell-System-XPS-L502X:~$ tkedit subject1 orig.mgz *tkedit: command not found* //======================================================================//
cheers Saurabh Thakur,
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,
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.
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,
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.
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.gztar: Unexpected EOF in archivetar: Unexpected EOF in archivetar: 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 fischl@nmr.mgh.harvard.eduwrote:
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 havenot 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.
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 srbhthkr@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 fischl@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 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,
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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Saurabh Thakur -
Sebastian Moeller