Hi, > We had the same problem with importing scans into Freesurfer that had been > converted from PAR/REC to NIFTI using nipy. The problem only affected a > subset of the data. When visualising the data with Fiji the brain appeared > highly skewed. Upon closer inspection of the header data of the NIFTI file we > discovered that there was an extra byte somewhere between the description > fields and the magic number sequence, causing the magic number to be > misinterpreted by Freesurfer. The extra byte was somewhere in the > transformation matrix that is located between the description field and the > magic number, but it's impossible to fix unless you know what the content of > the transformation matrix is supposed to be. However, when using dcm2nii, > part of mricron (from what I understand a newer version of mricro), to > convert our PAR/REC files to NIFTI the problem disappeared.
I'm the maintainer of nibabel so I guess I'm responsible for this bug... Can someone point me to a PAR / REC file that causes this problem? Private off-list is fine, but an image I can share for automated testing would be even better... Cheers, Matthew _______________________________________________ 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.
