> Hi Nick,
>
> I can't get the script to work but that might be due to my inexperience
> with matlab. I copied the script into my matlab directory, and tried to
> run
> dice_labels
> (/autofs/space/phrenic_007/users/jon/hires_amy/Round_1/HRDEV150/whole_amygdala.label,
> /autofs/space/phrenic_007/users/jon/hires_amy/Round_2/HRDEV150/whole_amygdala.label)
>
> But the error message said unexpected matlab operator.
>
> I then tried altering the script by substituting the actual labels for
> 'label1' and 'label2' but that didn't work either, and it gave me the same
> error message.
>
> Running the command alone, dice_labels, the error reads
>>> dice_labels
> ??? Input argument "lname1" is undefined.
>
> Error in ==> dice_labels at 29
> label1 = read_label('',lname1);
>
>
> I'm sure I'm doing something wrong, but no one in my group knows matlab
> well enough to figure it out.
>
>> Jon,
>>
>> Do the matlab scripts work for you? The approach you are taking with
>> the existing tools is the one I was considering myself but decided it
>> was too roundabout and probably wouldn't work for you anyway (because
>> mri_compute_seg_overlap looks for particular label ids corresponding to
>> subcortical structures), compared to the ease of just computing the dice
>> directly from the label files, which are just text files listing the
>> label coordinates.
>>
>> Nick
>>
>>
>> On Thu, 2009-08-20 at 14:09 -0400, [email protected] wrote:
>>> 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, [email protected] 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
>>> >> [email protected]
>>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >>
>>> >>
>>> >
>>>
>>>
>>
>>
>>
>
>
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