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 >> 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 >> > > > _______________________________________________ > 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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