Hi Doug and Bruce,

Adding the option "-proj frac 0 1 .0 " to mri_label2vol helps a lot; 
Just in case anyone needs it, the full command is :
mri_label2vol --label  label/lh.entorhinal_exvivo.label --temp mri/nu.mgz  --identity --o mri/lh-new-erc-filled-0.4.mgz --proj frac 0 1 .1 --subject bert --hemi lh 

I attached images of slices of the masks created with and without this option; The sum of the voxels in the mask i created is 1016 and is much closer to the volume 
the volume provided in lh.entorhinal_exvivo.stats (which is 925). I am curious why they are different? are there other advanced options in mri_label2vol I can try out ?



Thanks



Mehul



On Wed, Jun 26, 2013 at 4:11 PM, Mehul Sampat <mpsampat@gmail.com> wrote:
Hi Bruce, 
Yes, the one from label2vol "just hugs the white boundary"
Doug, I will try with the --proj frac 0 1 .1 option and let you all know. 
Thanks
Mehul




On Wed, Jun 26, 2013 at 3:58 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Oh, right. Mehul, you'll need to tell it to fill the ribbon with
something like --proj frac 0 1 .1
doug

On 06/26/2013 06:55 PM, Bruce Fischl wrote:
> won't the anatomical_stats one multiply thickness by surface area,
> where the label2vol will only fill voxels on the gray/white boundary,
> not all the way through the ribbon? Mehul: if you visualize the one
> from label2vol does it fill the ribbon or just hug the white boundary?
>
> On Wed, 26 Jun 2013, Douglas N Greve wrote:
>
>> not necessarily. That is a very small structure, and getting a few edge
>> voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in
>> tkmedit and load the surfaces too and see how good it did?
>> doug
>>
>> On 06/26/2013 06:49 PM, Mehul Sampat wrote:
>>> Hi Folks,
>>>
>>>
>>> I am trying to create an entorhinal cortex volume from
>>> ?h.entorhinal_exvivo.label using mri_label2vol
>>>
>>>
>>> I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is:
>>>
>>>
>>> *mri_label2vol --label  label/lh.entorhinal_exvivo.label --temp
> mri/nu.mgz  --identity --o mri/lh-new-erc.mgz*
>>>
>>>
>>>
>>>
>>>
>>> I took the sum of the voxels in this new mask i created
>>> (lh-new-erc.mgz) and it is 215;
>>> I looked at the volume provided inlh.entorhinal_exvivo.stats and it
>>> is 925; (from the log file I believe this is created using the command:
>>>
>>>
>>> mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b
>>> -l ./lh.entorhinal_exvivo.label bert lh white)
>>>
>>>
>>>
>>>
>>>
>>> I was expecting the numbers to  match orat-leastbe close; I am
>>> guessing I am using mri_label2vol incorrectly ?
>>>
>>>
>>> Could someone help me with this issue ?
>>>
>>>
>>> Thanks
>>>
>>>
>>> Mehul
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>>
>>
>
>

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