Thank you I will be thankful if you could let me know about the link related to recon-all, in order to know about the parameters(input volume info etc) associated to it and other usage. On Nov 19, 2014 12:18 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
> Hi Gunjan > > just run recon-all and it will do everything that we know how to do > (including those steps) > > cheers > Bruce > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > >> 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. > >
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