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That make sence. Thank you Mike!
 
So I think this commond on wiki was wrong

fslstats structural_bet_pve_1 -M -V | awk '{ print $1 * $3 }'

it should be

fslstats structural_bet_pve_1 -M -V | awk '{ print $1 * $2 }'

 
it should be $1 * $2,i.e., mean * # voxel, right?
 
 
Other questions:
1, did the pve images registered to templete space or kept in native space?
2, if I want to calculate ICV, i think it does not matter how much WM/GM/CFS in each voxel, can I just count nubmer of voxels in the brain and times it with size of voxel, i.e. second output of fslstats -V? Which image should I count on, the *pveseg*, *seg*,*mixeltype* or *brian*, *brain_mask* file? Or any file is ok for counting voxels? 
some paper said calculate ICV in this way:
To calculate intracranial  volume,  the  inverse  of  the  determinant  of  the  transformation matrix  was  multiplied  by  the  template  volume  (1,948,105  mm3)
It did not make sense to me, why ICV should be calculated on template then transfer to native space in some way?
 
Thanks for all your help!
 
Merry Christmas!
 
 
2013-12-25
Chunhui Chen
_________________
 
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875
发件人： Michael Dwyer
发送时间： 2013-12-25  04:39:28
收件人： FSL
抄送：
主题： Re: [FSL] How to use FAST to calculate volume?
Hi,

Maybe I'm reading it incorrectly, but I think what's confusing you is the nature of PVE files. They aren't binary maps, since each voxel can actually have more than one tissue type in it. The PVE image is coded from 0 to 1 continuously, and the intensity indicates the fraction of the voxel occupied by the specific type. So for example, a value of 0.3 on the GM PVE image (pve_1) means that that voxel has 30% of its volume occupied by GM (and the other 70% by other tissue). 

So, you can't just sum up the number of non-zero voxels and multiply by the voxel volume.

Hope that helps.

Best,
MIke


On Tue, Dec 24, 2013 at 10:41 AM, chenchunhuichina <[log in to unmask]> wrote:
Dear experts,
 
I am learning to use fast, on the wiki (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST ) you introduced how to calculate tissue volume, but I am just wondering why the volume is not number of voxels times size of each voxel, i.e., the second out put of -V?
Besides, I tried the commonds on the wiki with my data, but seems nubmers do not match.
 
Can anybody tell me what I was doing wrong, and how can I get to volume of white matter/ gray matter/ csf/ intracranial  volume correctly?
 
Thanks for any help!!
 
 
below was what I did
 
vol=`fslstats VG311_struc_pve_1 -V | awk '{ print $1}'`
mean=`fslstats VG311_struc_pve_1 -M`
tissuevol=`echo "$mean * $vol" | bc -l`
echo $tissuevol 
876788.096096
echo $mean
0.698489
echo $vol
1255264
 
fslstats VG311_struc_pve_1 -M -V | awk '{ print $1 * $3 }'
570833
 
below was what on the wiki

Tissue Volume Quantification

Estimating the tissue volume for a given class can be done using FAST and we recommend using the partial volume estimates for the most accurate quantification. The actual volume of tissue can be calculated easily from the corresponding partial volume map by summing up all the values. This can be done using fslstats and then multiplying the mean value by the volume (in voxels).

For example, for an image called structural_bet that fast was run on, the tissue volume of tissue class 1 can be found by running the following:

  • vol=`$FSLDIR/bin/fslstats structural_bet_pve_1 -V | awk '{print $1}'`

    mean=`$FSLDIR/bin/fslstats structural_bet_pve_1 -M`

    tissuevol=`echo "$mean * $vol" | bc -l`

    echo $tissuevol

This prints the total tissue volume in voxels (which is also stored in the variable tissuevol). Note that to get the volume in mm3 just replace the {print $1} with {print $2} in the first line above. Alternatively, this can be done in the single line:

  • fslstats structural_bet_pve_1 -M -V | awk '{ print $1 * $3 }'

 
 
 
2013-12-24
Chunhui Chen
_________________
 
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875



--
Michael G. Dwyer, Ph.D.
Assistant Professor of Neurology
Director of Technical Imaging Development
Buffalo Neuroimaging Analysis Center
University at Buffalo
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