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 <greve@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 > <fischl@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> > 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
