Calculating mean displacement from warp field

[Infinity]

Hi Gary,

As per my understanding a warp field contains for each voxel, how much the voxel has to be moved in x, y and z directions. The three volumes in a warp field contain this information for the three directions. So if the three volumes in the warp field are called X, Y and Z then for each voxel v, (X.v, Y.v, Z.v) is the displacement vector for that voxel. 

Is this correct? Or there's more to warp fields than that? If no, then to calculate the mean displacement I can get the displacement for each voxel and then just take the mean over all voxels right?

[Hui Zhang]

I think you have it right.  If you just need the mean displacement, you can use the tool VVMean to do that.

Gary

[Infinity]

By interoperability with FSL I mean, can I use FSL's fnirtfileutils to manipulate warp fields created by DTITK?

On Wed, Aug 1, 2012 at 3:12 PM, Infinity <19f1...@gmail.com> wrote:

Hi Gary,

Thanks for the reply. I tried using VVMean but it doesn't seem to be working properly, gave me the following error

bash-3.2$ VVMean -in abc.df.nii.gz -out temp

Thanks for using DTI-TK.  This version will expire in -305 days.

Please visit http://www.nitrc.org/projects/dtitk for the up-to-date version.

inFile = DTI_HN_pop.df.nii.gz
outFile = temp       6NãîîîîîwâBÜõ»»'+.ÄÝ
¸{BtöÜ©©¹#÷eÚÕP\>ë|k=¤°u«ÿ
GVíZ=SZµÿÏÇû¶­ÌþÇ
Åih({~¢Ü'ÍaïdzpêK#èr;·ÌH&¤0:1£p÷fÑh~Zƽ ,i,ÆÅòç_,s{ÇÑæu5¥ñܸO`BýãHØÚDî$9=µ¹3P÷É,­H!üF·a±¦-1½m¾mËÊ;z®°c==ì)ºeÏÝP>­và ÄÈT?uäwï÷:gíá4gºüu&­£·oº ãÊ¿®ô°r#j¦íÝ9ÙÛsÏÜYëAÕYn{rj«'l¼>ß±ÞüåÍ_ÞDôð¡õKLJ}wÃ)~=éGc¨?»öøåëzÙ"]®qýæa¡ÌÉÁ\Q    aã´
Reading ... ** ERROR (nifti_image_read): failed to find header file for '
Done in 0s
fail to load

There was also no documentation so I could not understand what VVMean does exactly. Does it take an average of the three volumes for each voxel? Does it take the euclidean norm of the vector? I noticed some other VV* tools that seemed useful. Is there a documentation for those?

Also, are the warp fields calculated by DTITK iteroperable in FSL and vice versa? Or, can I use DTITK to warp a scalar image?
 

[Infinity]

Hi Gary,

Thanks for the reply. I tried using VVMean but it doesn't seem to be working properly, gave me the following error

bash-3.2$ VVMean -in abc.df.nii.gz -out temp

Thanks for using DTI-TK.  This version will expire in -305 days.

Please visit http://www.nitrc.org/projects/dtitk for the up-to-date version.

inFile = DTI_HN_pop.df.nii.gz
outFile = temp       6NãîîîîîwâBÜõ»»'+.ÄÝ
¸{BtöÜ©©¹#÷eÚÕP\>ë|k=¤°u«ÿ
GVíZ=SZµÿÏÇû¶­ÌþÇ
Åih({~¢Ü'ÍaïdzpêK#èr;·ÌH&¤0:1£p÷fÑh~Zƽ ,i,ÆÅòç_,s{ÇÑæu5¥ñܸO`BýãHØÚDî$9=µ¹3P÷É,­H!üF·a±¦-1½m¾mËÊ;z®°c==ì)ºeÏÝP>­và ÄÈT?uäwï÷:gíá4gºüu&­£·oº ãÊ¿®ô°r#j¦íÝ9ÙÛsÏÜYëAÕYn{rj«'l¼>ß±ÞüåÍ_ÞDôð¡õKLJ}wÃ)~=éGc¨?»öøåëzÙ"]®qýæa¡ÌÉÁ\Q    aã´
Reading ... ** ERROR (nifti_image_read): failed to find header file for '
Done in 0s
fail to load

There was also no documentation so I could not understand what VVMean does exactly. Does it take an average of the three volumes for each voxel? Does it take the euclidean norm of the vector? I noticed some other VV* tools that seemed useful. Is there a documentation for those?

Also, are the warp fields calculated by DTITK iteroperable in FSL and vice versa? Or, can I use DTITK to warp a scalar image?
 

On Wed, Aug 1, 2012 at 12:25 AM, Hui Zhang <garyhu...@gmail.com> wrote:

[Hui Zhang]

Sorry, I assumed that you have used the similar tool for averaging the DTI volumes.  VVMean averages a set of displacement volumes.  So the input is a text file containing the filenames of the volumes that you want to average.  Here is an example

http://dti-tk.sourceforge.net/pmwiki/uploads/Documentation/subjs.txt

VVMean -in files.txt -out mean.df.nii.gz

In theory, you should be able to use DTI-TK's displacement fields with FSL.  If you want to warp scalar images, you can do this within DTI-TK as well.  This tutorial may give you a good idea on how to do so.

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.OptionspostReg

Gary

[Hui Zhang]

I'd think so.  DTI-TK uses the standard NIfTI format to store the displacement fields.  But I have not tried it myself.

Gary