Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

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 2

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

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 wrote I don't know that it would be preferred o

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

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 interpol

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

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 t

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

I think there is - look in the view menu. There is also something in freeview that Ruopeng can point you at. cheers Bruce On Sun, 27 Apr 2014, 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

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

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 t

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

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,

[Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

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 t