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 >> >> >> command (eg >> >> >> >> mritotal failed) >> while >> >> >> >> dealing with a >> specific set >> of >> volumes. >> >> How >> to >> >> >> >> overcome these >> issues in >> >> >> >> order to run >> recon-all >> >> successfully. >> >> >> >> Please find the >> >> recon-all.log >> and volume >> >> >> attached >> >> >> with >> this mail. >> >> >> >> >> Gunjan >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> 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. >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> 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 >> > > _______________________________________________ > 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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