[Mristudio-users] question using AIR in Landmarker

[Siewmin Gan]

Hi Susumu and Xin, many thanks. It works great.
Siewmin

On Sat, May 2, 2009 at 1:10 AM, susumu <susumu at mri.jhu.edu> wrote:

>  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
> >  > > _______________________________________________
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> >  > >  Mristudio-users at mristudio.org
> >  > >
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> >  >
> >  >
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> >
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