what is your mri_convert command line. Send the terminal output too. doug
On 01/31/2014 12:14 PM, Daniel Carey wrote: > Dear All, > > We have been using mri_convert to convert .nii format quantitative > scans (specifically R1 volumes) into .mgz (float) format, so they can > be used as input to mri_vol2surf. Inputting the .nii files to > mri_vol2surf has produced an error in values in the output paint file, > whereas this issue appears not to occur with the .mgz input. > > In running mri_convert, we are encountering an issue with the scaling > of image values. Optimally, we would like to preserve the values > within the quantitative volume, such that mri_convert does not change > these when we output to .mgz. In some cases, we have noted non-linear > differences in the output .mgz values, compared to the input volume. > We have been using the -ns flag, and still see these issues. > > Is there a way to set the output .mgz scale factor to preserve the > existing values exactly as per the quantitative input volume? > > Any advice would be greatly appreciated. Many thanks in advance. > > Best wishes, > Dan > > --- > > Daniel Carey > Marie Curie Ph.D. Fellow, > Centre for Brain and Cognitive Development, > 32 Torrington Sq., > London WC1E 7HX > UK > > email: d.ca...@bbk.ac.uk <mailto:d.ca...@bbk.ac.uk> > web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
