Ok I try this out using MATLAB. Thanks Bruce,
On Wed, Dec 17, 2014 at 7:32 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Gunjan > > I can't help you preserve it in minc and using someone else's tools to > convert slices to nifti. Can you work in matlb instead? If so, you can > convert the minc to .mgz with mri_convert, then load the mgz into matlab > using either MRIread or load_mgh (which will both return the direction > cosines), and save them with either MRIwrite or save_mgh, given preserving > the direction info. > > cheers > Bruce > > On Wed, 17 Dec 2014, Gunjan Gautam wrote: > > Hi Bruce, >> >> I am sorry that you could not get me properly. >> My query is, how can I preserve direction cosine information. As I am new >> to >> this issue, any help would really be appreciated. >> >> Thanks, >> Gunjan >> >> On Wed, Dec 17, 2014 at 7:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Gunjan >> >> our coordinate systems are extensively documented here: >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems? >> action=AttachFil >> e&do=get&target=fscoordinates.ppt >> >> cheers >> Bruce >> >> On Wed, 17 Dec 2014, Gunjan Gautam wrote: >> >> Hi Bruce, >> >> I can view the file using "freeview -v file.mnc" but >> I think that won't >> solve my problem as I need to switch from 2D to 3D >> and vice versa. >> I will be thankful if you could be a bit specific >> about "preserving the >> direction cosine information" as I am facing >> difficulty to process these >> volumes through FS. >> >> >> Thanks, >> Gunjan >> >> On Tue, Dec 16, 2014 at 7:59 AM, Gunjan Gautam >> <gunjan.gemin...@gmail.com> >> wrote: >> >> Thank you Bruce, >> >> I try this out. >> >> On Dec 16, 2014 7:58 AM, "Bruce Fischl" >> <fis...@nmr.mgh.harvard.edu> wrote: >> I'm not sure what to tell you then. You need >> to save it in >> a format that preserves the direction cosine >> information. >> This shouldn't be that hard to do (e.g in >> matlab) >> Bruce >> >> >> On Tue, 16 Dec 2014, Gunjan Gautam wrote: >> >> >> I think that won't resolve my issue >> because I >> need to deal with a specific >> set of noise removal algorithms and >> nonuniformity correction algorithms. >> >> On Dec 16, 2014 7:50 AM, "Bruce Fischl" >> <fis...@nmr.mgh.harvard.edu> wrote: >> have you tried just giving the >> original >> volume to recon-all? We >> typically deal with this kind of >> thing >> internally (and in 3D, >> not on a slice-by-slice basis) >> >> cheers >> Bruce >> On Tue, 16 Dec 2014, Gunjan Gautam >> wrote: >> >> >> Sure, >> >> My data(3D volume) is having >> different ranges of >> noise and nonuniformity so >> I want to apply different >> algorithms to get rid of >> these and analyze the >> extent. >> >> On Dec 16, 2014 7:40 AM, >> "Bruce >> Fischl" >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Gunjan >> can you elaborate? >> What kind >> of modifications >> would you want to >> make to each slice? >> >> Bruce >> On Tue, 16 Dec 2014, >> Gunjan >> Gautam wrote: >> >> >> Yes Bruce, minc >> is a >> volume but I want >> to perform >> some experiments >> and >> see >> the >> aftereffects. >> This is how I >> come >> from 3D to 2D to make >> changes in >> each slice and >> again I >> rejoin these >> slices >> (2D to 3D). I don't >> know if >> anything other >> than >> NIfTi >> gives this much >> flexibility or it could >> be dealt >> without coming >> in 2D >> space. >> >> Any suggestion >> will be >> highly >> appreciate. >> >> On Dec 16, 2014 >> 7:22 >> AM, "Bruce Fischl" >> >> <fis...@nmr.mgh.harvard.edu> wrote: >> isn't the >> minc a >> volume? It >> certainly supports >> holding an >> entire >> volume in >> a >> single file >> On Tue, 16 >> Dec >> 2014, Gunjan Gautam >> wrote: >> >> >> Ok , >> I try >> this out. >> >> I >> converted it to nii >> because after >> processing 2D >> >> slices of >> the volume, I >> can >> easily >> switch to 3D >> space(ie >> stacking) in >> order >> to >> apply >> brain >> >> extraction >> tools as NIfTi >> provides some >> of the >> >> useful >> utilities. >> >> On >> Dec 16, >> 2014 6:59 AM, >> "Bruce Fischl" >> >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> >> why >> do you need to >> convert it to >> nifti? Can >> you >> process the minc >> >> >> directly? See if >> freeview can >> display it: >> >> >> >> freeview -v file.mnc >> >> >> >> >> On >> Tue, 16 Dec 2014, >> Gunjan Gautam >> wrote: >> >> >> >> >> Hi Bruce, >> >> >> >> Originally, data >> was in MINC >> format. >> >> >> >> On Dec 16, 2014 >> 1:54 AM, >> "Bruce Fischl" >> >> >> >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> >> >> Hi Gunjan >> >> >> >> what was >> the original >> data format >> that >> you >> >> >> had? Once you >> have >> >> >> converted >> it to nifti >> in your >> >> current >> stream >> >> >> you can no >> longer >> >> >> use the >> data, so you >> have to start >> >> further >> >> >> upstream >> >> >> >> cheers >> >> >> Bruce >> >> >> >> >> On Tue, 16 >> Dec 2014, >> Gunjan Gautam >> >> wrote: >> >> >> >> >> I >> don't have >> dicom for this >> >> subject >> but >> >> >> it can >> >> >> >> easily be >> converted to >> from >> >> >> .nii >> to .dcm. >> >> >> I >> try this out >> and get back >> to >> you if >> I >> >> >> stuck at >> >> >> some >> point. >> >> >> >> >> Thanks, >> >> >> >> Gunjan >> >> >> >> On >> Dec 16, 2014 >> 12:49 AM, >> >> "Bruce >> Fischl" >> >> >> >> >> <fis...@nmr.mgh.harvard.edu> >> >> wrote: >> >> >> >> do you >> have the dicom >> data >> for >> >> >> this subject? >> >> >> If >> so, it will >> be >> >> >> >> separated >> into >> >> different >> "series" >> >> >> each >> >> >> >> corresponding to >> one >> >> >> >> >> acquisition >> (e.g. a >> >> T1-weighted >> >> >> one such as >> >> >> >> mprage or >> FLASH). >> >> >> >> Typically >> that series >> will >> have >> >> >> more than 150 >> >> >> >> slices (since >> >> >> >> that's >> what it takes >> to >> cover >> the >> >> >> brain at >> >> >> >> close to 1mm >> voxel >> >> >> >> size). You >> need to >> give >> recon-all >> >> >> the dicom >> >> >> file >> that >> contains a >> >> >> >> single one >> of those >> >> slices. It >> >> >> doesn't matter >> >> >> >> which one - we >> >> >> >> will >> figure out the >> rest >> of >> them >> >> >> from any of >> >> >> them >> >> >> >> >> On Tue, 16 >> Dec 2014, >> >> Gunjan >> Gautam >> >> >> wrote: >> >> >> >> >> >> Hi >> Bruce, >> >> >> >> >> I am >> sorry to >> say >> that I >> did >> >> >> not get you >> >> >> >> properly. >> >> >> >> >> Could you please >> say >> a bit >> >> >> more about "a >> >> >> >> *single* >> >> >> >> >> slice in the >> >> correct >> >> >> >> >> series ". I want >> to >> try >> this >> >> >> option. >> >> >> >> >> On >> Dec 16, 2014 >> >> 12:13 AM, >> >> >> "Bruce Fischl" >> >> >> >> >> >> <fis...@nmr.mgh.harvard.edu> >> >> >> wrote: >> >> >> >> >> Hi Gunjan >> >> >> >> >> >> freesurfer >> will >> handle >> >> >> the dicom >> >> >> >> slices just >> >> >> >> >> find. Just give >> >> >> >> >> recon-all >> a >> *single* >> >> >> slice in the >> >> >> >> correct >> >> >> >> >> series with the >> -i >> >> >> >> >> command >> and >> it >> should >> >> >> work. I >> >> >> >> don't know >> >> >> >> >> medcon, but it >> is >> not >> >> >> >> >> >> >> propagating the >> >> >> direction cosine >> >> >> info >> into the >> >> >> >> >> nifti, which >> >> >> >> >> means that >> the >> nifti >> >> >> files are >> >> >> >> effectively >> >> >> >> >> useless as you >> will >> >> >> >> >> never be >> able >> to >> >> >> distinguish left >> >> >> from >> right >> >> >> >> >> again >> >> >> >> >> >> cheers >> >> >> >> >> Bruce >> >> >> >> >> >> >> On Tue, 16 >> Dec >> 2014, >> >> >> Gunjan Gautam >> >> >> >> wrote: >> >> >> >> >> >> >> >> >> Thanks >> Bruce, >> >> >> >> >> >> I >> used >> "medcon" >> >> >> command >> >> >> >> (Ubuntu) for the >> >> >> >> >> stacking of >> >> >> >> >> 2D >> >> slices in >> >> >> order to >> >> >> >> >> >> >> convert it >> in a >> >> >> volume. >> >> >> >> These slices >> >> >> >> were >> obtained >> >> >> >> >> from >> a >> volume >> >> >> itself and >> > > > _______________________________________________ > 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. 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