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. > >
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