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. This is the reason I used mri_convert command.
If I am not wrong then recon-all command will do bias correction as well, which is not my requirement. What I want is to have the binary brain mask volume and brain volume only. recon-all command is asking for the subject-id and I'm not sure about it. I have gone through its documentation but still not able to run it properly. I request you to please help me in this. Regards, Gunjan On Wed, Nov 19, 2014 at 6:50 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Gunjan > > you need to give us more details. What are you trying to do? Why not just > run recon-all -all? That will be much easier than trying to ru individual > steps > > chers > Bruce > > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > Hi, >> >> I am facing few issues. I will be thankful if you can help me out. >> >> Query 1) I used "mri_convert a.nii a.resliced.nii -rl b.nii" in order to >> generate slices so that comparison may take place properly. The command >> ran >> properly but generating cropped slices. >> I am attaching the input volume, reference volume and the cropped slice >> screenshot. >> [icon_10_generic_list.png] a.nii >> >> [icon_10_generic_list.png] b.nii >> >> >> >> Query 2) For skull stripping I ran below command >> bibl04@BIBL04:~/Desktop/freesurfer/bin$ recon-all -i a.nii -autorecon1 >> and its showing error for subject id. I am really not aware, what to >> write. >> ERROR: must specify a subject id >> >> Query 3) I did not find that which option from (1 to 31 ) should generate >> the "binary brain mask". >> >> >> Thanks, >> Gunjan >> >> On Wed, Nov 19, 2014 at 12:41 AM, Gunjan Gautam < >> gunjan.gemin...@gmail.com> >> wrote: >> >> Ok, I go through that. >> >> Thanks, >> Gunjan >> >> On Nov 19, 2014 12:37 AM, "Bruce Fischl" >> <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Gunjan, >> >> it's all on the wiki. You should go through our >> tutorials >> >> cheers >> Bruce >> On Wed, 19 Nov 2014, Gunjan Gautam wrote: >> >> >> 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. >> >> >> >> _______________________________________________ >> 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. > >
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