John,
Also, I think you may need to include the flag '-ns 1' in the mri_convert command when converting aseg.mgz files to any other format, otherwise there is a possibility of resampling, which changes the label values.
Nick
On Thu, 2008-10-16 at 12:47 -0400, Bruce Fischl wrote:
Hi John,
sorry, I'm not sure exactly what you mean. Do you for example to copy just the hippocampus from the aseg? Or the voxels in the orig.mgz that correspond to the aseg? Or some cortical ROIs? How are you currently doing the conversions? We need details like command lines and outputs.
cheers, Bruce
On Thu, 16 Oct 2008, John Pluta wrote:
I have been trying to use FreeSurfer to automatically generate several ROIs for me. This is easy with the autosegment feature. However, I need to be able to work with them in Analyze or Nifti format. So far, any kind of conversion method has gotten me ROIs that are not the same as the results of autosegmentation. In every case, whether I extract a single roi or try to convert the whole set at once, there is a great deal of noise in the resulting Nifti file. This is obvious just by looking, and you can also see the discrepency by looking at the voxel count of the converted ROI versus the voxel count in the stats file produced by autosegmentation- there is typically a difference of hundreds of voxels.
I've tried all of the methods in the tutorials and slides, and everything I could find in the mailing list so far. Everything comes out to this same result. Has anybody else encountered this or had any luck? Also, does anyone know the source of the noise in the converted images? If I could trace where that comes from, maybe I could write some kind of script to repair the ROIs I need.
Thank you.
-John _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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