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>* 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>>* 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> > > 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> > > 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
_______________________________________________ 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.
