[Mristudio-users] [Fwd: short course]

[Xin Li]

Hi Steen,

After you resample the ROI data, if the size of the resampled ROI image is the same as the one before being resampled, you can use the roi header file for the resampled ROI file after you change the file name of the header file. For example, if the name of the roi file is mouse.dat and the name of the resampled roi file is resampledmouse.dat, you can change the name of the header file for the roi file from mouse.roihdr to resampledmouse.roihdr. Then you can load the resampled roi data as ROIEditor-defined format in ROIEditor. In this way, you can keep the lable information.

If the size of the resampled ROI image is not the same as the original one, you can click the button "Change ROI File Header" that is in the ROI section of the tool panel. This function can change the size information stored in the header file. Please also change the name of the header file to the same name as the resampled roi file. Then you can load the resampled roi data as ROIEditor-defined format in ROIEditor. The label information will be displayed in the roi object list.

Hope this can help you.


Xin


----- Original Message -----
From: "Pedersen, Steen E." <sepeders at texaschildrens.org>
Date: Wednesday, January 22, 2014 11:35 am
Subject: [Mristudio-users]  [Fwd: short course]
To: "mristudio-users at mristudio.org" <mristudio-users at mristudio.org>
Cc: "Pedersen, Steen E. (BCM)" <pedersen at bcm.edu>


> Dear Support
>                  First, thanks for writing such a powerful and useful 
> set of programs. I have a question regarding the mouse brain atlas maps.
>  
>  The segmentation of the mouse brain appears very useful. I am 
> processing data from a number of users doing mouse brain. 
> Unfortunately, for each experiment, the exact dimensions of each set 
> of scans can vary as can the mouse age.
>      I have been using the mouse atlas for registration to a standard 
> mouse so as to compare groups of mice objectively. This is fine, and I 
> can resample the standard mice easily in diffeomap.
>                  My question is whether there is a simple way to 
> resample the segmentation maps for the mouse brain. This would give me 
> a powerful way to quickly get detailed information back to the user. I 
> can resample the raw ROI data, but I lose the label information (ei - 
> the objects become "object 1, object 2, etc" instead of 
> "hippocampus-L, hippocampus-R, etc".
>  Other than typing it in each time, is there a way to import the 
> labels into ROIeditor to get them back? I have tried using a new 
> header, but it doesn't seem to preserve the object labels.
>  
>  If there is a more detailed manual for ROIeditor, I would greatly 
> appreciate a pointer for it as I see it being a very useful tool for 
> my work.
>  
>  Thank you,
>  Steen Pedersen
>  (registered email: pedersen at bcm.edu)
>  
>  Steen E. Pedersen, Ph.D.
>  Associate Professor
>  Small Animal Imaging Facility
>  
>  Phone: 832-824-3399
>  Cell: 713-726-0041
>  email: sepeders at texaschildrens.org
>  
>  Feigin Center, Room C.0200.02
>  Texas Childrens Hospital
>  1102 Bates St., Houston, TX 77030
>  
>  éala éarendel engla beorhtast
>  
>  
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