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=AttachFile&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 >> >> >> >> >> after >> making >> >> some intensity >> >> >> changes, a >> >> >> >> volume is >> >> >> >> >> formed >> (using >> >> medcon) >> >> >> >> >> again. >> Then I >> >> fed this >> >> >> volume as input >> >> >> to >> FS in >> >> >> >> >> order to >> extract >> >> brain. >> >> >> >> >> Can >> I >> overcome >> >> this >> >> >> orientation >> issue ? >> >> >> >> >> >> Gunjan >> >> >> >> >> On >> Dec 15, >> 2014 >> >> 11:49 PM, >> >> >> "Bruce Fischl" >> >> >> >> >> >> >> <fis...@nmr.mgh.harvard.edu> >> >> >> wrote: >> >> >> >> >> Hi >> Gunjan >> >> >> >> >> >> the >> >> problem is that >> >> the >> nifti >> >> >> >> volume doesn't >> >> >> >> >> contain >> the >> >> >> >> >> >> direction >> >> cosine >> >> >> information that >> >> >> we >> need to >> >> >> >> >> figure out >> what >> >> >> >> >> >> directions >> >> are A/P, >> >> I/S >> and L/R. >> >> >> >> mri_convert >> >> >> >> >> warns of >> this: >> >> >> >> >> >> >> >> mri_convert >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz >> >> >> >> >> test.mgz >> >> >> >> >> >> >> mri_convert >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz >> >> >> >> >> test.mgz >> >> >> >> >> $Id: >> > > > _______________________________________________ > 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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