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 >> 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. 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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 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 not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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