No, once you've got the orientation correct, then it should be fine On 04/29/2014 08:03 PM, prasser wrote: > Other than orientation, (which could be deduced from visual inspection > of fiducial markers or other) are there any other concerns with this > approach? > Paul > > > ---- On Tue, 29 Apr 2014 09:04:00 -0700 *Douglas N Greve > <gr...@nmr.mgh.harvard.edu>* wrote ---- > > > I don't know that it would be preferred or acceptable. You have just > thrown away information about what is left and right, so you might > have > inadvertently flipped the brain. Unless your voxel size is 1mm, there > will be some interpolation when conforming. I'm not that worried > about > the interpolation artifact that you see in tkmedit/freeview > > doug > > > On 04/28/2014 11:53 PM, prasser wrote: > > > > Thanks. > > > > Using: > > > > mri_convert dicom output.nii -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0 > > > > > > Seems to do the trick. > > > > I have attached a figure with the left image from mri_convert > and the > > right image using mri_convert and the flags listed above, both > viewed > > using tkmedit. > > > > > > From a visual perspective I prefer the right hand image, and > wonder if > > this striping appearance in the left hand image is smoothed when > > creating orig.mgz using the --conform flag? > > > > Would using: > > > > mri_convert dicom output.nii -iid 0 -1 0 -ijd 0 0 -1 -ikd -1 0 0 > > > > mri_convert output.nii orig.mgz --conform > > > > be preferred (or acceptable) in this case? > > > > Paul > > > > > > ---- On Mon, 28 Apr 2014 14:55:27 -0700 *Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>* > wrote ---- > > > > > > I don't think this is aproblem either. tkmedit/freeview will be > > showing > > it in the acquisition RAS space (not the image coordinate space). I > > don't think there is anything wrong with the actual data. If the > > volumes > > from other packages do not show up this way in tkmedit/fv then > it may > > mean that they are throwing away this information. You can throw > > it away > > too when you run mri_convert, something like > > > > mri_convert dicom output.nii -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 > > > > see if that at least causes the funny images to go away. > > > > > > On 04/27/2014 10:35 PM, prasser wrote: > > > Thanks for your reply. > > > > > > Yes, I can upload the data. Is there a private area I can upload > > to? > > > > > > Also, is there a flag that enables acquisition slice space info > > to be > > > used with tkmedit? > > > > > > Lastly, when converting to .nii with other packages and viewing > > with > > > tkmedit the acquisition slice space seems to be taken into > account. > > > > > > Paul > > > > > > > > > > > > > > > > > > ---- On Sun, 27 Apr 2014 17:33:02 -0700 *Bruce Fischl > > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu>>* wrote ---- > > > > > > Hi Paul > > > > > > perhaps Ruopeng can comment, but I suspect this isn't a problem - > > > it's > > > just showing it to you in a standard anatomical space not the > > > slice spaceit > > > was acquired in. If you want to upload the dataset we can take a > > > look and > > > confirm > > > > > > cheers > > > Bruce > > > > > > > > > On Sun, 27 Apr 2014, prasser wrote: > > > > > > > Hi, > > > > > > > > I am still having some concerns using mri_convert on Skyra > > > volumes that I'm > > > > hoping can please be addressed. > > > > > > > > On this occasion I have used mri_convert to convert a single > > > dicom file to > > > > nifti from a volume collected on a siemens Skyra scanner using > > > Freesurfer5.3 > > > > on CentOS5.7. > > > > > > > > When viewing this nifti image using tkmedit it appears 'cut-up' > > > over many > > > > sagittal slices (please see attached) rather than the whole > > > image appearing > > > > on one plane. > > > > > > > > Not sure if this is an issue with tkmedit or mri_convert? > > > > > > > > This problem persists if i convert the entire volume, with this > > > 'cutting' > > > > appearing as vertical lines in the image. > > > > > > > > This is also the case when using the new mri_convert patch for > > > OS X. > > > > > > > > Lastly, I can upload a dicom file if needed. > > > > > > > > Thanks, > > > > Paul > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
