Try adding --empty

On 4/12/2021 4:58 PM, miracle ozzoude wrote:

External Email - Use Caution

Hello Experts,

I am using mri_segstats with the --ctab flag to extract dti and suvr values from a white matter hyperintensities parcellation. Running mri_segstats on the image and parcellation with --ctab only reports on non-empty segmentations. I want it to also report on the empty segmentations.

Is there a flag or any other freesurfer commands that i can use?

Summary: I want mri_segstats to report on non-empty and empty segmentations, not just the former.

Cheers. || |cmdline mri_segstats --seg wmh_lobar.nii.gz --i subj_rescaled_wholecere_PET2T1_smooth.nii.gz --sum SUVR_WMH_lobar.stats --ctab WMColorLUT.ctab --pv norm.mgz| |Loading wmh_lobar.nii.gz| |INFO: using NIfTI-1 qform| |Loading subj_rescaled_wholecere_PET2T1_smooth.nii.gz| |Loading norm.mgz| |Voxel Volume is 1 mm^3| |Generating list of segmentation ids| |Found 13 segmentations| |Computing statistics for each segmentation||Reporting on 11 segmentations| |Using PrintSegStat| |mri_segstats done|

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer