[Mristudio-users] quantifying motion and batch job

[susumu mori]

Hi all,

For batch processing, quality control has been the biggest issue for us.
We've been investing our time on methods to evaluate many different sources
of image deterioration (please see "DtiStudioUpdate.doc" at
https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2) and correction.

It is only recently we start to feel comfortable to use a fixed pipeline.
Currently we are working on quantitative reporting of quality control, which
may take several months to deliver. I believe it may pave a way for fully
automated processing (command line or single-click).

So, please wait for release of the full-feature command-line version.
Meanwhile, Hangyi may provide a current command line version, although it
may not support some functions.

Susumu

On Thu, Aug 19, 2010 at 7:40 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hello Hangyi,
>
> My apologies for hijacking Weihong's thread, but I would also be very
> interested in a command line version of the program.  Can you please let me
> know where I can find it.  I would be happy to report back bug reports to
> help improve it.
>
> Thank you,
> Jeff
>
> On Thu, Aug 19, 2010 at 7:04 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi Weihong,
>>
>>
>>  1. After registering the DWIs to b0, is there anyway to get some
>>> quantification about the motion?It would be great if we can get the frame by
>>> frame motion "magnitude" (rotation, translation, skew) data in the form of a
>>> text file. Is there a existing function available in DTIStudio that can
>>> allow me to do that?
>>>
>>
>> Please see https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2.
>> There you can find a *.doc file explaining how you can check the motion
>> correction results. In reality, the cross-contrast registration like b0-DWI
>> is difficult and it is difficult to expect perfect registration. However, as
>> the file explains, mutual information, although it takes longer, tends to
>> perform better. AIR also has a strong dependence on threshold value.
>>
>> We are working on quantitative reporting of the registration results.
>> Currently there is an option to save the transformation matrix in the text
>> format.  When you start AIR, at the bottom of the AIR window, there is "Save
>> transformation matrix" in the "Other" section.
>>
>>
>>> 2. Is there a beta version of the software that can do some batch work? I
>>> understand the quality checking for bad frame/slice/pixel always needs human
>>> decision, as you have mentioned before. What about batch job for motion/eddy
>>> current correction, or other procedure that may not need as much human
>>> expertise?
>>>
>>
>> Hangyi has a command-line version of the software. It may not support all
>> the functions, but please contact him.
>>
>>
>>>
>>> Thanks in advance
>>>
>>> Weihong
>>>
>>>
>>> Weihong Yuan, Ph.D.
>>> Research Assistant Professor/McLaurin Fellow
>>> Pediatric Neuroimaging Research Consortium
>>> Imaging Research Center, Dept. of Radiology
>>> Cincinnati Children's Hospital Research Foundation
>>> 3333  Burnet Ave.
>>> Cincinnati, OH 45229
>>> Phone: 513-636-2862
>>> FAX: 513-636-0434
>>>
>>>
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>>
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