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 > > _______________________________________________ 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.
