batch_reset_orientation help for PASL acquired P>A orientation

[Ashwati Vipin]

Hello, 

I'm very new to ASL imaging and have been working with the ASLtbx using the PASL test scripts. I'm running the batch_reset_orientation step and am a little confused. The manual says that the GUI (3.1 Reorient the images") is obsolete since I am using SPM12. So I moved straight to section 4 and I am step 4.2 (resetting and setting origins).  This step talks about about "batch_generateorigintable" and "origintable.m" but I am unable to find these scripts in the pasl_sie_spm12 folder. Also, the ASLtbx_resetimgorgASL.m script says that the function will only work if:

% be careful for using the following lines: this will only

% work if the data were acquired or saved from right to

% left, from anterior to posterio and inferior to superior

% vox(1)=-abs(vox(1));

% vox(2)=-abs(vox(2));

However, the 3D PASL data I have collected was acquired from P>>A orientation. Could you please help me understand how I should amend the "batch_reset_orientation" script for my data? 

Thanks so much for your help.

Best,

Ashwati

[red...@gmail.com]

Hi Ashwati,

     Resetting orientation has been switched from the manual approach (which needs the origintable.m) to an automatic way using “batch_reset_orientation.m”.  The latest version from my website should work for data acquired from all three vendors.  (you can also get the code from my github: https://github.com/zewangnew/ASLtbx) The question you have below regards to the image orientation for some old images (especially in old times when the Nifti format had some issues for recording the image orientation correctly).  You don’t need to uncomment the two lines.   The main goal of reseting orientation is to change the image origin to the center of the image box.  Nothing else.  

 

Please try one sample data from your own and let me know if the toolbox works.

 

Ze

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