Re: [Freesurfer] dimensions swapped with head first-prone acquisition {Disarmed}

[Caspar M. Schwiedrzik]

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Great, thanks a lot, Doug!
Caspar

On Tue, May 7, 2019 at 17:46 Greve, Douglas N.,Ph.D. 
wrote:

> The --in_orientation should work. The RAS coordinates will reflect subject
> space (which is probably what you want) and  not scanner space.
>
> On 5/7/2019 11:27 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi!
> I have data acquired on a Siemens scanner with head first-prone. When I
> convert the dicom files to MGZ, left and right and superior and inferior,
> respectively, are swapped. The anterior-posterior dimension is ok. I am
> wondering what the correct way to correct this is?
>
> Following this entry in the wiki
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
> ,
> it seems that I can use mri_convert with --in_orientation for that, and the
> images indeed look correct when I do this. I am however wondering whether I
> have to do the conversion to COR and fix the RAS coordinates as well?
> I found a 2007 entry on the mailing list about that
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.html
> ,
> but it does not specify how to proceed.
>
> Your advice would be appreciated!
> Thanks, Caspar
>
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Re: [Freesurfer] dimensions swapped with head first-prone acquisition

[Greve, Douglas N.,Ph.D.]

The --in_orientation should work. The RAS coordinates will reflect subject 
space (which is probably what you want) and  not scanner space.

On 5/7/2019 11:27 AM, Caspar M. Schwiedrzik wrote:

External Email - Use Caution

Hi!
I have data acquired on a Siemens scanner with head first-prone. When I convert 
the dicom files to MGZ, left and right and superior and inferior, respectively, 
are swapped. The anterior-posterior dimension is ok. I am wondering what the 
correct way to correct this is?

Following this entry in the wiki 
https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal, it seems that I 
can use mri_convert with --in_orientation for that, and the images indeed look 
correct when I do this. I am however wondering whether I have to do the 
conversion to COR and fix the RAS coordinates as well?
I found a 2007 entry on the mailing list about that 
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.html, 
but it does not specify how to proceed.

Your advice would be appreciated!
Thanks, Caspar



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[Freesurfer] dimensions swapped with head first-prone acquisition

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I have data acquired on a Siemens scanner with head first-prone. When I
convert the dicom files to MGZ, left and right and superior and inferior,
respectively, are swapped. The anterior-posterior dimension is ok. I am
wondering what the correct way to correct this is?

Following this entry in the wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal, it seems that
I can use mri_convert with --in_orientation for that, and the images indeed
look correct when I do this. I am however wondering whether I have to do
the conversion to COR and fix the RAS coordinates as well?
I found a 2007 entry on the mailing list about that
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.html,
but it does not specify how to proceed.

Your advice would be appreciated!
Thanks, Caspar
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