You can use mri_convert to change the orientation in the header. If you run mri_convert without options it will give you lots of documentation doug

On 7/18/14 9:17 AM, Fan, Qiuyun wrote:

Hi Doug,

I think I figured it out. It's the angulation of the image plane. ImageOreintation (should have been axial slices) reads "0.99995101907245\0.00923454555106-0.0035612672513-0.0089978930043\0.69829945291611-0.7157491962821", and was thus identified as coronal. So, nothing went wrong with mri_convert.

As a follow up question, although technically, there's nothing wrong with it, it does look confusing intuitively. I'm wondering if there's a way to fool the nifti to label it as LPS at all?

Thanks a lot!

Best,

Qiuyun ________________________________________ From: Fan, Qiuyun Sent: Thursday, July 03, 2014 4:19 PM To: Douglas N Greve Subject: mri_convert

Hi, Doug,

I found an error when using mri_convert to convert image from dicom to nifti. I have one odd subject, whose orientation labels were wrong. The dicom-info-dump looks the same as the other subjects, and the images look fine too.

If you have a chance to take a look at the images, here's the path to the "odd" subject:/autofs/cluster/hcps/data_preproc/HCPS_017/dcm/diff_1k/

An example of a "good" subject can be found here: /autofs/cluster/hcps/data_preproc/HCPS_015/dcm/diff_1k/

BTW, I'm using /usr/local/freesurfer/stable5_3_0.

Please let me know if you need more information from me.

Thanks a lot!

Best,

Qiuyun