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: >> mri_convert.c,v >> >> 1.213 >> >> >> 2014/07/29 >> 19:22:31 >> >> >> >> fischl Exp $ >> >> >> >> reading >> from >> >> >> >> >> >> >> >> >> >> >> >> >> >> m000-stacks-m000-t1_icbm_normal_1mm_pn0_rf0-00001.nii.gz... >> >> >> >> WARNING: >> neither >> >> NIfTI-1 qform or >> >> >> sform are >> >> >> >> valid >> >> >> >> WARNING: >> your volume >> will >> probably >> >> be >> >> >> >> incorrectly >> oriented >> >> >> >> TR=1.00, >> TE=0.00, >> >> TI=0.00, flip >> >> >> angle=0.00 >> >> >> >> WARNING: >> it does not >> >> appear that >> >> >> there was >> >> >> >> sufficient >> >> >> >> >> information >> >> >> >> in the >> input to assign >> >> orientation >> >> to >> the >> >> >> >> volume... >> >> >> >> i_ras = >> (-1, 0, 0) >> >> >> >> j_ras = >> (0, 1, 0) >> >> >> >> k_ras = >> (0, 0, 1) >> >> >> >> writing to >> test.mgz... >> >> >> >> >> and if you >> try to view >> the >> >> >> converted volume >> in >> >> >> >> freeview it >> shows >> >> >> >> up in the >> wrong >> >> orientation (e.g >> >> what >> we think >> >> >> is >> "coronal" is >> >> >> >> actually >> horizonatal). >> >> >> >> >> How did >> you create the >> >> nifti >> >> >> files? If you >> >> >> give >> dicom >> directly >> >> >> >> to >> recon-all you >> will >> >> likely not >> >> have >> this >> >> >> >> problem >> >> >> >> >> cheers >> >> >> >> Bruce >> >> >> >> >> >> On Thu, 11 >> Dec 2014, >> >> Gunjan Gautam >> >> >> wrote: >> >> >> >> >> ​Dear >> all, >> >> >> >> >> I am >> facing few >> >> errors in >> >> >> recon-all >> >> > > > _______________________________________________ > 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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