I downloaded two volumes from BrainWeb database. One is treated as ground truth because it has preassigned values(0-11) for each types of tissues and by a simple coding binary brain mask can be achieved. Another volume is the processed one using any brain extraction algorithm. Now, I have two volume one is standard and another processed one. I want to observe the performance of the algorithm that how much accurate which needs to compare both the volumes, pixel by pixel. This comparison will take place properly only when both volumes will generate same number of slides. I am stuck here. Now, ground truth is generating equal number of slides as of the processed volume but these are getting cropped (please see the attached jpg file in previous mail) . Hi Gunjan
you need to give us more information. What are the two volumes? Why is one "ground truth"? What in general are you trying to achieve? cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: > I have attached both the volumes (reference and input) with my mail. > Its the last step of my work, I'm stuck at and not finding any solution. I > read that FreeSurfer can solve my problem. > > I will be obliged if you find some time for this. > > Best Regards, > Gunjan > > On Nov 19, 2014 8:19 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > wrote: > no, because I don't know what the volume are that you are using > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > > Ok I try this out. > > Did you answer my Query 1(related to cropped output > of mri_convert command ? > I probably did not understand. > > On Nov 19, 2014 8:10 PM, "Bruce Fischl" > <fis...@nmr.mgh.harvard.edu> wrote: > Hi Gunjan > > FreeSurfer has been designed to work as a > pipeline. Picking out > individual pieces and running them may or may > not work, and > certainly won't be as reliable. I would advise > you to run > recon-all -all, then you can use the contents > of the subject > directory to do whatever analyses you want > (e.g. generate an > un-bias-corrected, skull stripped volume). > > The subject id is one that you make up - it > will be the name of > the directory under which the results are > stored. Also specify a > SUBJECTS_DIR on the command line, which will > be the root > directory under which all the individual > subject trees live > (with -sd <subjects directory path> > > cheers > Bruce > > > On Wed, 19 Nov 2014, Gunjan Gautam wrote: > > 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 > _______________________________________________ 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.
