Ranjan, I installed Fedora21 onto a laptop. I then download and installed freesurfer and, after installing a few basic packages (tcsh libXcrnSaver), I was able to open freeview without any errors.
Which means the "library not found" issue you are encountering has something to do with your local environment. Either the filesystems you are mounting or the extraction errors you encounter when untarring. As Daniel suggests, you may want to confine this to your local disk. -Zeke On 04/15/2015 10:03 AM, dgw wrote: > Ranjan, > > You may want to try installing it on a local hard disk. Do you have > any scratch space you can use on the computer? > > HTH, > D > > On Tue, Apr 14, 2015 at 5:09 PM, Ranjan Maitra > <maitra.mbox.igno...@inbox.com> wrote: >> Nick, >> >> Thanks! It does match in the gzipped tarball: >> >> ~$ md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz >> 6642289df823ebc27de52af57e9b3989 >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz >> >> ~$ md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar >> 8cf47fbcd0a675f7832986ee87c2d00f >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar >> >> I don't think that this matters, but the filesystem is an Inselon OneFS >> filesystem and is mounted on to my machine via a cifs mount. >> >> Many thanks, >> Ranjan >> >> >> >> >> >>> -----Original Message----- >>> From: ni...@nmr.mgh.harvard.edu >>> Sent: Tue, 14 Apr 2015 16:26:50 -0400 >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 >>> >>> Ranjan, >>> >>> after downloading, confirm the integrity of the tarball by running >>> md5sum on it. you should get the following sum: >>> >>> 6642289df823ebc27de52af57e9b3989 >>> >>> also, make sure you have at least 4.2GB of space prior to download. >>> some older partitions have a 4GB max size (probably not the case, but >>> thought i'd mention it). >>> >>> Nick >>> >>> On Tue, 2015-04-14 at 12:06 -0800, Ranjan Maitra wrote: >>>> Zeke, >>>> >>>> Thanks! >>>> >>>>> >>>>> 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. >>>> >>>> Thank you very much! >>>> >>>>> >>>>> 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. >>>> >>>> I agree with you, but I have tried downloading and unpacking several >>>> times, to no avail. Always the same error/message. (I use wget, but I >>>> don't see why that should be a problem.) I can not see how to get around >>>> this. Do you have any other suggestions as to how to get around this? >>>> >>>> Many thanks, >>>> Ranjan >>>> >>>> >>>> >>>> >>>>> 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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It stores your passwords & protects your >>>>>> account. >>>>>> Check it out at http://mysecurelogon.com/password-manager >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> ____________________________________________________________ >>>> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! >>>> Check it out at http://www.inbox.com/earth >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> ____________________________________________________________ >> 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
