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 >> 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... >> > > > _______________________________________________ > 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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