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. 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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. > >
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