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
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
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 greve@nmr.mgh.harvard.eduwrote:
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 greve@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
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