Ranjan, At the present moment I am unsure what the exact problem is. It currently appears as though Fedora 21 is not recognizing the "libvtkverdict.so.5.6" shared library. This might be a Linux kernel incompatibility given that Fedora 21 was released just months ago, but libvtkverdict was compiled around 5 years ago, on a system with much older version of the kernel.
We support centos6 platform but we are currently unaware of any linux distributions in which freeview can not open. I dont not have immediate access to a Fedora21 system but I will attempt to install one and investigate this further. Please allow a day or so for a response. Lastly, it would make me feel a lot better if you could extract the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz without getting any errors. Its possible something is getting corrupted along the way which is somehow responsible for this issue. -Zeke On 04/14/2015 03:15 PM, Ranjan Maitra wrote: > Zeke, > > Thanks again! > >> -----Original Message----- >> From: zkauf...@nmr.mgh.harvard.edu >> Sent: Tue, 14 Apr 2015 15:12:06 -0400 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 >> >> Ranjan, >> >> Ok, the binaries appear work. So at the present moments the issue >> appears to only be with libvtkverdict.so.5.6.0 >> >> 1) What happens if, right before you type the freeview command, you set >> the LD_LIBRARY_PATH environment variable as follows: >> >> (if bash) >> $> export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6 >> $> freeview > > I tried this, to no avail: > > ~$ export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > ~$ freeview > freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: > cannot open shared object file: No such file or directory > > >> >> (if csh) >> $> setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 >> $> freeview >> >> 2) What is the output when you perform an 'md5sum' on >> libvtkverdict.so.5.6.0 >> >> $> cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 >> $> md5sum libvtkverdict.so.5.6.0 > > ~$ cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > ~$ md5sum libvtkverdict.so.5.6.0 > 4daa2098074db45b5729d3c68e167f96 libvtkverdict.so.5.6.0 > > Thanks again! > > Best wishes, > Ranjan > > >> >> >> On 04/14/2015 02:55 PM, Ranjan Maitra wrote: >>> Thanks! It works, in the sense that it goes to completion: >>> >>> ~$ mri_convert sample-001.mgz test.mgh >>> mri_convert sample-001.mgz test.mgh >>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >>> reading from sample-001.mgz... >>> TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 >>> i_ras = (-0, -1, -0) >>> j_ras = (-0, 0, -1) >>> k_ras = (-1, 0, 0) >>> writing to test.mgh... >>> >>> ~$ >>> >>> Best wishes, >>> Ranjan >>> >>>> -----Original Message----- >>>> From: zkauf...@nmr.mgh.harvard.edu >>>> Sent: Tue, 14 Apr 2015 14:44:34 -0400 >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 >>>> >>>> Ranjan, >>>> >>>> What happens when you try to use the mri_convert binary? >>>> >>>> $> cd $FREESURFER_HOME/subjects >>>> $> mri_convert sample-001.mgz test.mgh >>>> >>>> -Zeke >>>> >>>> On 04/14/2015 12:07 PM, Ranjan Maitra wrote: >>>>> Hi, >>>>> >>>>> it is: >>>>> >>>>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >>>>> >>>>> Many thanks, >>>>> Ranjan >>>>> >>>>>> -----Original Message----- >>>>>> From: zkauf...@nmr.mgh.harvard.edu >>>>>> Sent: Tue, 14 Apr 2015 10:43:54 -0400 >>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>> Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 >>>>>> >>>>>> Ranjan, >>>>>> >>>>>> What is the contents of you $FREESURFER_HOME/build-stamp.txt file? >>>>>> >>>>>> On 04/13/2015 08:15 PM, Ranjan Maitra wrote: >>>>>>> This does not change anything, but it appears that in either case, >>>>>>> the >>>>>>> directory is untarred. (I can not tell if the error matters.) So I >>>>>>> wanted to go further and see about running the examples in: >>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview >>>>>>> >>>>>>> I have a new problem: the libraries on Fedora are too new for the >>>>>>> ones >>>>>>> required in the package (eg libvtkverdict.so.5.6.0). However, the >>>>>>> package itself appears to have these libraries. So, my question is: >>>>>>> how/where do I set the path for these libraries? >>>>>>> >>>>>>> I want to get around errors like the following: >>>>>>> >>>>>>> freeview.bin: error while loading shared libraries: >>>>>>> libvtkverdict.so.5.6: cannot open shared object file: No such file >>>>>>> or >>>>>>> directory >>>>>>> >>>>>>> The libraries appear to be in $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 >>>>>>> >>>>>>> Where should I change the pathname to be set this? >>>>>>> >>>>>>> Many thanks and best wishes, >>>>>>> Ranjan >>>>>>> >>>>>>> >>>>>>>> -----Original Message----- >>>>>>>> From: zkauf...@nmr.mgh.harvard.edu >>>>>>>> Sent: Fri, 10 Apr 2015 19:51:25 -0400 >>>>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>>>> Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 >>>>>>>> >>>>>>>> Try using gunzip first. Then untarring. >>>>>>>> >>>>>>>> >>>>>>>>> On Apr 10, 2015, at 2:05 PM, Ranjan Maitra >>>>>>>>> <maitra.mbox.igno...@inbox.com> wrote: >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I have a strange issue, trying to install the 64-bit tgz onto >>>>>>>>> Fedora >>>>>>>>> 21. >>>>>>>>> >>>>>>>>> So, I downloaded using wget: >>>>>>>>> >>>>>>>>> $ wget -c >>>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz >>>>>>>>> >>>>>>>>> But when i unrar, I get to the very last file extraction (as per >>>>>>>>> tar >>>>>>>>> tzf) and get: >>>>>>>>> >>>>>>>>> $ tar zxvf >>>>>>>>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz >>>>>>>>> ...... >>>>>>>>> freesurfer/fsfast/toolbox/binomialpdf.m >>>>>>>>> tar: Exiting with failure status due to previous errors >>>>>>>>> >>>>>>>>> >>>>>>>>> What is the issue here? >>>>>>>>> >>>>>>>>> Many thanks, >>>>>>>>> Ranjan >>>>>>>>> >>>>>>>>> ____________________________________________________________ >>>>>>>>> FREE ONLINE PHOTOSHARING - Share your photos online with your >>>>>>>>> friends >>>>>>>>> and family! >>>>>>>>> Visit http://www.inbox.com/photosharing to find out more! >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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. 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