Hi Nick,
I was actually able to convert the label files into volumes using
mri_label2vol and then use the mri_segstats to get the total number of
pixels from each volume file. But the mri_compute_seg_overlap didn't
work as easily. I tried running the following but the results were all
zero, which I've included as well:
mri_compute_seg_overlap -olog text whole_amygdala_test.mgz
../../Round_2/HRDEV150/whole_amygdala_test2.mgz
logging overall Dice to text
Jaccard Coefficients:
correct ratio for label 2 = 0
correct ratio for label 41 = 0
correct ratio for label 3 = 0
correct ratio for label 42 = 0
correct ratio for label 4 = 0
correct ratio for label 43 = 0
correct ratio for label 17 = 0
correct ratio for label 53 = 0
correct ratio for label 10 = 0
correct ratio for label 49 = 0
correct ratio for label 11 = 0
correct ratio for label 50 = 0
correct ratio for label 12 = 0
correct ratio for label 51 = 0
correct ratio for label 13 = 0
correct ratio for label 52 = 0
correct ratio for label 18 = 0
correct ratio for label 54 = 0
correct ratio for label 26 = 0
correct ratio for label 58 = 0
correct ratio for label 14 = 0
correct ratio for label 15 = 0
correct ratio for label 5 = 0
correct ratio for label 44 = 0
mean +/- std = 0.0000 +/- 0.0000
Dice Coefficients:
label 2 = 0
label 41 = 0
label 3 = 0
label 42 = 0
label 4 = 0
label 43 = 0
label 17 = 0
label 53 = 0
label 10 = 0
label 49 = 0
label 11 = 0
label 50 = 0
label 12 = 0
label 51 = 0
label 13 = 0
label 52 = 0
label 18 = 0
label 54 = 0
label 26 = 0
label 58 = 0
label 14 = 0
label 15 = 0
label 5 = 0
label 44 = 0
mean +/- std = 0.0000 +/- 0.0000
Overall subcortical dice = nan
Any ideas?
Thanks
> Jon,
>
> None of the existing utilities will calculate the Dice of two labels (at
> least not in a straightforward manner). However, its easy to do in
> matlab.
>
> Attached is a script to do this. Copy it to your
> $FREESURFER_HOME/matlab directory.
>
> Usage is:
>
> dice_labels('label1.label','label2.label')
>
> or just
>
> dice_labels('label1','label2')
>
>
> this assumes the two labels were created in the same volume.
>
> Nick
>
>
>
> On Thu, 2009-08-20 at 12:21 -0400, jen...@nmr.mgh.harvard.edu wrote:
>> Hi,
>>
>> I need to compute the reliability of two manually traced ROIs and I
>> was
>> told to use the command mri_compute_seg_overlap. However, it seems
>> this command needs its input to be in .mgz format, but the ROIs have
>> been saved as .label files in Freeview. A simple renaming function
>> does not work, so is there another way to make mri_compute_seg_overlap
>> work with .label files? Thanks.
>>
>> Best,
>> Jon
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
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