[Mristudio-users] question using AIR in Landmarker

[susumu]

Hi Siewmin,

 

I hope Xin is working on the error message you got. 

I just want to comment on your "Screenshot1". In this window, the template
is T1 and your data to be normalized is FA. 

I recommend to use the same contrast. For example, you can use b0 (T2) or
DWI for both template and your data. 

There are two ways to normalize FA;

1) you can load both DWI (or b0) and FA. Choose DWI in active window before
you start AIR. After AIR all leaded images (in this case FA) will also be
normalized based on the DWI-DWI (or b0-b0) intra-contrast AIR result. Avoid
cross-contrast AIR as much as possible.

2) you can do DWI-DWI (or b0-b0) AIR and save the AIR output file
(transformation matrix). Later, you can load FA, ADC, or whatever images you
want to normalize. Then apply the AIR transformation matrix using the button
with "M coming out of a folder" button in the "Volume LDDMM" section.

 

  _____  

From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Siewmin Gan
Sent: Friday, May 01, 2009 1:35 AM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: Re: [Mristudio-users] question using AIR in Landmarker

 

Hi Xin thanks. I have attached a few shots here with a brief description.

1. the landmarker window where I clicked on the "align button" at the bottom
left corner

2. The folder where I would save the output file (filename: AlignWarpOutput
and filetype:(*.warp)). This folder is in my Computer/Local Disk/Landmarker
(i.e C:/Landmarker) where I have placed the Landmarker software and the .exe
files.

3. In snapshot 3, i change the save as type file to all files, so you can
see that the align_warp.exe and other .exe files are also in this folder.

4. The snapshot of the 1st error msg. When I clicked "OK", the second error
message occur as shown in shot 5. 

 

Initially, I did get a warning message that there should be no spaces in the
whole path of the warp file etc, and have resolved that error message. 

 

Many Thanks

 

Siewmin 

 

On Fri, May 1, 2009 at 12:02 AM, Xin Li <xli16 at jhmi.edu> wrote:

Siewmin,

Could you take snapshots of these two error messages? And please tell me the
whole path of the warp file that you were going to save on your machine. The
whole path of the warp file should not have any spaces. I am not sure if
this is the reason.



Xin



----- Original Message -----
From: Siewmin Gan <siewmin.gan at gmail.com>

Date: Thursday, April 30, 2009 11:31 am
Subject: Re: [Mristudio-users] question using AIR in Landmarker
To: "DTI Studio, ROI Editor, Landmarker Questions/Support"
<mristudio-users at mristudio.org>


> Hi Xin, the error message occurs in a pop up warning window on the
DTIstudio
>  GUI.
>  thanks
>
>  Siewmin
>
>  On Wed, Apr 29, 2009 at 11:30 PM, Xin Li <xli16 at jhmi.edu> wrote:
>
>  > Siewmin,
>  >
>  > Where did you see this error message "C:/Landmarker/align_warp.exe.
> The
>  > parameter is incorrect" ? Did you see it in the C command window or
> in a pop
>  > up warning window?
>  >
>  >
>  > Xin
>  >
>  >
>  >
>  > ----- Original Message -----
>  > From: Siewmin Gan <siewmin.gan at gmail.com>
>  > Date: Thursday, April 23, 2009 5:08 am
>  > Subject: [Mristudio-users] question using AIR in Landmarker
>  > To: mristudio-users at mristudio.org
>  >
>  >
>  > > Hi,    I'm trying to do non-linear registration to normalise my
resampled
>  > >  aDWI images to the ICBM_DTI_81 DWI template. When I clicked on the
>  > "align
>  > >  button", I recieved two error messages (below), and could not
perform
>  > > the
>  > >  registration step:
>  > >
>  > >  "C:/Landmarker/align_warp.exe. The parameter is incorrect"
> followed by
>  > >  "cannot find warp file".
>  > >
>  > >  I have placed the aligned_warp.exe file in the folder landmarker
> where
>  > >  software is located, and am not sure where the problem may be.
>  > >
>  > >  Many Thanks
>  > >
>  > >  Siewmin
>  > > _______________________________________________
>  > >  Mristudio-users mailing list
>  > >  Mristudio-users at mristudio.org
>  > >
>  > _______________________________________________
>  > Mristudio-users mailing list
>  > Mristudio-users at mristudio.org
>  >
>  >
> _______________________________________________
>  Mristudio-users mailing list
>  Mristudio-users at mristudio.org
>
_______________________________________________
Mristudio-users mailing list
Mristudio-users at mristudio.org
http://lists.mristudio.org/mailman/listinfo/mristudio-users

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20090501/c7d3f19c/attachment.html