Dear Freesurfer experts
When I ran: mris_anatomical_stats -i 0 0.002 -l label/lh.roi.label -t / surf/lh.MD.mgh -b -f stats/lh.roi.stats subid lh to get the DTI value for a particular label, the function does not really take the thresholds I set into account as it displayed: only considering thicknesses in the range [0.0,0.0].
Is it because the range I want to detect is too small?
Also, the result is always 0.001(mean DTI) +/-0.000 (std) for all the subjects and all the different labels.
Thank you very much!
Lily
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On 12/18/2013 12:08 PM, Hamza Alshuft wrote:
Dear Freesurfer experts
When I ran: mris_anatomical_stats -i 0 0.002 -l label/lh.roi.label -t / surf/lh.MD.mgh -b -f stats/lh.roi.stats subid lh to get the DTI value for a particular label, the function does not really take the thresholds I set into account as it displayed:
only considering thicknesses in the range [0.0,0.0].
You can ignore this. It is just a display error in that it only prints out 1 digit past the decimal, so the upper limit gets rounded to 0.0, but internally it will use 0.0 and 0.002.
Is it because the range I want to detect is too small?
Also, the result is always 0.001(mean DTI) +/-0.000 (std) for all the subjects and all the different labels.
This is also probably a rounding/precision error in the output. I might use a combination of mri_binarize and mri_segstats for this. Eg,
mri_binarize --i lh.MD.mgh --min 0 --max .002 --o lh.MD.mask.mgh mri_segstats --mask lh.MD.mask.mgh --slabel subject lh lh.roi.label --id 1 --sum lh.roi.stats See if that gives you better results. If the precision of the digits in lh.roi.stats is not good enough, you can add --mul 100 to multiply everything by 100.
doug
Thank you very much!
Lily
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Douglas N Greve -
Hamza Alshuft