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. 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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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