Ok, I try this tomorrow morning. I will be thankful if you could tell me about getting brain mask and performing skull stripping otherwise I'll have to wait for 12 hours to get your replies as our working hours doesn't match. On Nov 18, 2014 8:45 PM, "Z K" <zkauf...@nmr.mgh.harvard.edu> wrote:
> Gunjan, this may be related to an Ubuntu specific issue we address on > the Freesurfer download page: > > https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > Specifically the part thats states the following: > > *** > On Ubuntu, you might have to do this if qdec or freeview complain about > libjpeg or libtiff: > > cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) > sudo ln -s libjpeg.so.8 libjpeg.so.62 > sudo ln -s libtiff.so.4 libtiff.so.3 > *** > > -Zeke > > > > > On 11/18/2014 03:55 AM, Gunjan Gautam wrote: > > Hello Sir, > > > > I have place the "license.txt" in the same directory that contains > > build-stamp.txt as there were no directory with name "FREESURFER_HOME". > > freeview command is not working and showing below message > > "freeview.bin: error while loading shared libraries: libjpeg.so.62: > > cannot open shared object file: No such file or directory". > > What next I need to do in order to generate a output brain mask. > > > > Best Regards, > > Gunjan > > > > > > > > On Thu, Nov 13, 2014 at 12:24 AM, Z K <zkauf...@nmr.mgh.harvard.edu > > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: > > > > Im having a little difficulty following all the avenues of your > attempts > > to get this working, but the bottom line is that the error message > below > > is complaining that you do not have a valid license file. > > > > You need to go to this page and register and get the valid license > file: > > > > https://surfer.nmr.mgh.harvard.edu/registration.html > > > > Once you get a valid license file you will need to place it in your > > $FREESURFER_HOME directory (the same directory that contains > > build-stamp.txt) and give it the name .license or license.txt. Try > both. > > > > -Zeke > > > > On 11/12/2014 01:29 PM, Gunjan Gautam wrote: > > > Sir earlier I was trying to use FreeSurfer using Virtual Box in my > > > Windows machine. There the mri_convert command did not work so I > > > switched to a Linux machine. Now, I'm using centos6_x86_64 version > as my > > > machine has the Ubuntu 12.04 platform and here also facing the same > > > problem. > > > > > > I want to share one thing that in my institute I tried hard to > download > > > FreeSurfer but every time it resulted into a time-out situation so > I had > > > to ask someone to get it downloaded and send me through Google > drive. > > > This was how I installed it in my system. > > > > > > Best regards, > > > Gunjan > > > > > > On Nov 12, 2014 9:15 PM, "Z K" <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu> > > > <mailto:zkauf...@nmr.mgh.harvard.edu <mailto: > zkauf...@nmr.mgh.harvard.edu>>> > > wrote: > > > > > > Gunjan, > > > > > > Are you using your own version of VirtualBox, with freesurfer > installed > > > on it by you? Or the VirtualBox version of freesurfer made by > us and > > > downloaded from our website? I am confused because in your > email below, > > > freesurfer appears to be installed on the Desktop whereas the > > > prepackaged version made by us is installed in /usr/local > > > > > > -Zeke > > > > > > On 11/12/2014 08:54 AM, Gunjan Gautam wrote: > > > > Hello Sir, > > > > > > > > License file is present in the folder but with the name > LICENSE. > > > Should > > > > I download it again ? > > > > > > > > Best Regards, > > > > Gunjan > > > > > > > > On Nov 12, 2014 7:01 PM, "Bruce Fischl" > > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu > > > > <mailto:fis...@nmr.mgh.harvard.edu <mailto: > fis...@nmr.mgh.harvard.edu>> > > > > <mailto:fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu> > > > <mailto:fis...@nmr.mgh.harvard.edu > > <mailto:fis...@nmr.mgh.harvard.edu>>>> wrote: > > > > > > > > Hi Gunjan > > > > > > > > do you have a license? If not you need to download and > > install it > > > > (as noted in the error message). They are free. > > > > > > > > cheers > > > > Bruce > > > > On Wed, 12 Nov 2014, Gunjan Gautam wrote: > > > > > > > > > > > > Hello Sir, > > > > > > > > I'm using FreeSurfer through Virtual Box. I tried > > the below > > > > command for > > > > reslicing my volume according to a reference > > volume but the > > > > process gets > > > > stuck at " reading volume". > > > > > > > > mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz > > > > > > > > A: Volume to be resampled / resliced > > > > B: Reference Volume > > > > > > > > Error message is being shown like below: > > > > > > > > mri_convert a.nii a.resliced.nii -rl b.nii > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > > > mreuter Exp $ > > > > reading from a.nii... > > > > > > > > > > > ------------------------------__------------------------------__-------------- > > > > ERROR: Invalid FreeSurfer license key found in > > license file > > > > > > /home/bibl04/Data_Home/__Desktop/freesurfer/license.txt > > > > If you are outside the NMR-Martinos Center, > > > > go to http://surfer.nmr.mgh.harvard.__edu > > > > <http://surfer.nmr.mgh.harvard.edu> to > > > > get a valid license file (it's free). > > > > If you are inside the NMR-Martinos Center, > > > > make sure to source the standard environment. > > > > > > > > Actually, I have two volumes, belong to the same > > subject. One > > > > volume is the > > > > ground truth which will be considered as standard > > for the > > > second > > > > volume > > > > which is the processed one or the extracted brain. > To > > > perform a > > > > perfect > > > > comparison between both volumes, these must > > generate equal > > > > number of slices > > > > in order to compare the corresponding slide. But > here > > > there is > > > > problem with > > > > my volumes, that is while performing slicing > > Ground Truth > > > volume is > > > > generating 360 slice and processed volume is > > generating 181 > > > > slides. So > > > > comparison can't take place in this way. > > > > > > > > What all I need is to do the resampling or > > generating the 181 > > > > slides from > > > > the Ground Truth as well. > > > > > > > > > > > > Best Regards, > > > > Gunjan > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: > 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 <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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 >
_______________________________________________ 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.
