Hi, Thanks for your response. When I tried that option I got the same results, and I looked at the output header file and it still said ‘float32.’ I tried removing the -nc option, but that messed it up worse. None of my other attempts at tweaking the command are working thus far.
Is there anything else I can try? Thank you, David From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, February 21, 2012 12:58 AM To: David Grayson Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] weird relabeling with mri_convert Try -odt short to stop it from changing the data type to uchar On Feb 21, 2012, at 12:04 AM, David Grayson <gray...@ohsu.edu<mailto:gray...@ohsu.edu>> wrote: Hi freesurfer folks, I am using mri_convert to reorient my custom cortical parcellation (a nifti file generated from an annotation file), and I have run into some unexpected blips with some seemingly errant reindexing. Here is the command I am using: mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz For the most part, this works well for most of the indices. The biggest problem is that the highest value index (2063) is being completely relabeled in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s range. But this occurs to a smaller extent with many of the other regions as well, where small parts of those regions are being relabeled with values anywhere from 1 to 20. Can anyone give me some insight as to what’s up with this and what I might be able to do to fix it? Thank you very much for any help. -David _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
_______________________________________________ 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.
