Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

2017-04-25 Thread Douglas Greve 
The missing/extra are due to sub-1mm estimation. They do not exist 
independently. If you want to avoid partially volumed voxels, you can 
erode the segmentation to remove border voxels



On 4/25/17 2:50 PM, Gamaliz wrote:

For example.
I register another image to the aseg+aparc file and do some 
pixel-by-pixel calculations; reading the regions from the aseg+aparc 
and matching them on the registered file (in this case a DTI) ie: 
every pixel with value 2 in aseg+aparc belongs to the 
Left-Cerebral-White-Matter region.


however, as the aseg+aparc is missing some pixels (or have extra ones) 
depending on how the pixel count differs from the volume (as reported 
in the aseg.stats file), I will have either missing (extra) pixels.



Maybe I am asking too much? :/


On Tue, Apr 25, 2017 at 2:45 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


more exact than what?


On 4/25/17 2:07 PM, Gamaliz wrote:

Is there any way to generate a file which is more exact? Or
perhaps, is that file already there?

On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

The aseg.stats is generated with partial volume estimation


On 4/25/17 12:40 PM, Gamaliz wrote:

I wrote an algorithm which uses the number of pixels per
region in the aseg+aparc.mgz file. As this file has 1x1x1mm3
I was expecting the number of pixels to match very closely
the value of the volume; as each pixel represents a 1 mm3
cube.(I did the same for cortical volume and got a similar
result, with an even larger discrepancy).

The aseg.stats file lists the nVoxel value, and it is
basically the volume rounded up.
here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz):
7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in
aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz):5899

Pretty much the values are close to the volume, but
different enough to be significant. I wonder why this
discrepancy.


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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

2017-04-25 Thread Gamaliz 
For example.
I register another image to the aseg+aparc file and do some pixel-by-pixel
calculations; reading the regions from the aseg+aparc and matching them on
the registered file (in this case a DTI) ie: every pixel with value 2 in
aseg+aparc belongs to the Left-Cerebral-White-Matter region.

however, as the aseg+aparc is missing some pixels (or have extra ones)
depending on how the pixel count differs from the volume (as reported in
the aseg.stats file), I will have either missing (extra) pixels.


Maybe I am asking too much? :/


On Tue, Apr 25, 2017 at 2:45 PM, Douglas Greve 
wrote:

> more exact than what?
>
> On 4/25/17 2:07 PM, Gamaliz wrote:
>
> Is there any way to generate a file which is more exact? Or perhaps, is
> that file already there?
>
> On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve 
> wrote:
>
>> The aseg.stats is generated with partial volume estimation
>>
>> On 4/25/17 12:40 PM, Gamaliz wrote:
>>
>> I wrote an algorithm which uses the number of pixels per region in the
>> aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
>> of pixels to match very closely the value of the volume; as each pixel
>> represents a 1 mm3 cube.(I did the same for cortical volume and got a
>> similar result, with an even larger discrepancy).
>>
>> The aseg.stats file lists the nVoxel value, and it is basically the
>> volume rounded up.
>> here are some sample values for subcortical regions:
>>
>> Left-Lateral-Ventricle Volume (mm3): 7829.8
>> Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
>> Left-Inf-Lat-Vent Volume (mm3):594
>> Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
>> Left-Cerebellum-White-Matter Volume (mm3):12668
>> Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
>> Left-Cerebellum-Cortex Volume (mm3):44113.2
>> Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804
>> Left-Thalamus-Proper Volume (mm3):5752.8
>> Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899
>>
>> Pretty much the values are close to the volume, but different enough to
>> be significant. I wonder why this discrepancy.
>>
>>
>> ___
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>> information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
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>> sender and properly dispose of the e-mail.
>
> --
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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

2017-04-25 Thread Douglas Greve 

more exact than what?


On 4/25/17 2:07 PM, Gamaliz wrote:
Is there any way to generate a file which is more exact? Or perhaps, 
is that file already there?


On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


The aseg.stats is generated with partial volume estimation


On 4/25/17 12:40 PM, Gamaliz wrote:

I wrote an algorithm which uses the number of pixels per region
in the aseg+aparc.mgz file. As this file has 1x1x1mm3 I was
expecting the number of pixels to match very closely the value of
the volume; as each pixel represents a 1 mm3 cube.(I did the same
for cortical volume and got a similar result, with an even larger
discrepancy).

The aseg.stats file lists the nVoxel value, and it is basically
the volume rounded up.
here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in
aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz):5899

Pretty much the values are close to the volume, but different
enough to be significant. I wonder why this discrepancy.


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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

2017-04-25 Thread Gamaliz 
Is there any way to generate a file which is more exact? Or perhaps, is
that file already there?

On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve 
wrote:

> The aseg.stats is generated with partial volume estimation
>
> On 4/25/17 12:40 PM, Gamaliz wrote:
>
> I wrote an algorithm which uses the number of pixels per region in the
> aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
> of pixels to match very closely the value of the volume; as each pixel
> represents a 1 mm3 cube.(I did the same for cortical volume and got a
> similar result, with an even larger discrepancy).
>
> The aseg.stats file lists the nVoxel value, and it is basically the volume
> rounded up.
> here are some sample values for subcortical regions:
>
> Left-Lateral-Ventricle Volume (mm3): 7829.8
> Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
> Left-Inf-Lat-Vent Volume (mm3):594
> Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
> Left-Cerebellum-White-Matter Volume (mm3):12668
> Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
> Left-Cerebellum-Cortex Volume (mm3):44113.2
> Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804
> Left-Thalamus-Proper Volume (mm3):5752.8
> Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899
>
> Pretty much the values are close to the volume, but different enough to be
> significant. I wonder why this discrepancy.
>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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> dispose of the e-mail.
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Re: [Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

2017-04-25 Thread Douglas Greve 

The aseg.stats is generated with partial volume estimation


On 4/25/17 12:40 PM, Gamaliz wrote:
I wrote an algorithm which uses the number of pixels per region in the 
aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the 
number of pixels to match very closely the value of the volume; as 
each pixel represents a 1 mm3 cube.(I did the same for cortical volume 
and got a similar result, with an even larger discrepancy).


The aseg.stats file lists the nVoxel value, and it is basically the 
volume rounded up.

here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz):43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz):5899

Pretty much the values are close to the volume, but different enough 
to be significant. I wonder why this discrepancy.



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[Freesurfer] Relation between Segmentation Volumes and number of pixels in Aseg+aparc.mgz

2017-04-25 Thread Gamaliz 
I wrote an algorithm which uses the number of pixels per region in the
aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
of pixels to match very closely the value of the volume; as each pixel
represents a 1 mm3 cube.(I did the same for cortical volume and got a
similar result, with an even larger discrepancy).

The aseg.stats file lists the nVoxel value, and it is basically the volume
rounded up.
here are some sample values for subcortical regions:

Left-Lateral-Ventricle Volume (mm3): 7829.8
Left-Lateral-Ventricle (number of Pixels in aseg+aparc.mgz): 7396
Left-Inf-Lat-Vent Volume (mm3):594
Left-Inf-Lat-Vent(number of Pixels in aseg+aparc.mgz):569
Left-Cerebellum-White-Matter Volume (mm3):12668
Left-Cerebellum-White-Matter(number of Pixels in aseg+aparc.mgz):12203
Left-Cerebellum-Cortex Volume (mm3):44113.2
Left-Cerebellum-Cortex(number of Pixels in aseg+aparc.mgz): 43804
Left-Thalamus-Proper Volume (mm3):5752.8
Left-Thalamus-Proper(number of Pixels in aseg+aparc.mgz): 5899

Pretty much the values are close to the volume, but different enough to be
significant. I wonder why this discrepancy.
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