I've isolated the problem to a fsl utility fslreorient2std I used to get the brains to view right-side-up in fslview. I don't get the error when not using this utility. mri_convert is cleared, I think. Josh
On Fri, Aug 10, 2012 at 8:15 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > what are your exact mri_convert commands? > doug > > On 08/09/2012 06:05 PM, Joshua Lee wrote: > > I used mri_convert to resample my norm.mgz to 0.25 mm iso nii.gz, and > > then again back up to 1mm isotropic space. The resultant image shifted > > up a voxel from the original converted straght to nii.gz. This points > > to the resampling procedure, and not the conversion to different file > > format. Suggestions? > > > > Note: I wanted to hand trace the hippocampus in the norm.mgz, and > > upsampled the norm.mgz to trace on. I traced it, and then downsampled > > to 1mm to compare with Freesurfer segmentation, but found it shifted. > > Josh > > > > > > > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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. > >
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