[Mristudio-users] command file

[susumu mori]

Hi Jeff,

we are working on the command-line programs, but if I'm not mistaken, the
current commands are limited to the pre-processing of the images such as
changes matrix and resolution conversion, translation, and rotation.

DiffeoMap does image registration and our experience tells it is still
difficult to automate the process because quality control at each step is
essential.

Susumu

On Mon, Apr 5, 2010 at 10:18 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hello Everyone,
> I am interested in using the command/script based files to run a lot of
> datasets.  I read Xin's posting about doing this in DiffeoMap with the
> following commands.  Is there anywhere I can look to see all of the
> available commands?  And are the instructions the same for DTI Studio as
> they are for DiffeoMap?
>
> Thank you!
> Jeff Sadino
>
>
> Govind,
>
> You need to create a command txt file named as "xx.cf" first. The attached
> is an example. It decribes the syntax of the commands. The Load Command File
> option process all the loaded subject images based on these commands.
>
> Hope this will help you.
>
> Xin
>
>
> //.cf file Format
>
> // Lines that begin with "//" are comment lines.
> // Commands are enclosed by "Begin/End" clauses.
>
> // The commands use reserved keywords, such as "crop", "format",
> "orientation".
>
> // Crop Slices in Axial Projection Command Syntax
> // crop startslicenumber endslicenumber
>
> // Change Format Command Syntax
> // format byte(word, float)
>
> // Change Slice Orientation Command Syntax
> // orientation axial(sagittal, coronal)
>
> // Rotate Image Command Syntax
> // rotate x degree y degree z degree trilinear(neighbor)
>
> // Shift Image Command Syntax
> // shift point(mm) x shift y shift z shift
>
> // Resample Image Command Syntax
> // resample imagewidth imageheight numberofslices fovwidth fovheight
> slicethickness trilinear(neighbor)
>
> // example
>
> //    Begin
> //        crop 20 180
> //        format byte
> //        orientation axial
> //        rotate x 45 y 0 z 10 neighbor
> //        shift point x 10 y 0 z 5
> //        resample 181 217 181 181 217 1 trilinear
> //    End
>
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