Reorient function in DPARSFA

Submitted by Mamtis13 on Fri, 11/22/2013 - 01:56

Dear experts,

I have a couple of questions regarding the 'T1 dicom to Nifti' function as well as the reorient boxes which are marked with an asterisk in the DPARSFA toolbox. It would be very helpful if you had any comments or details on the following issues:

  1. When converting T1 dicom files to Nifti, the T1Img folder contains 3 files (t1*.nii, cot1*.nii, ot1*.nii). I understand that this process uses Chris Rorden's dcm2nii script. Can you please confirm that the ot1*.nii file is the reoriented T1 image and that the cot1*.nii image is the cropped, reoriented T1 image? Can you please tell me how the reorientation and cropping is achieved, i.e. what are the processes involved for reorienting and cropping the T1 image? 
  2. When do I need to check the 'Reorient Fun*', 'Reorient T1*' and/or the 'Reorient after Coregistration*' boxes? I understand that this involves some interactive, manual reorientation. Is this correct? When would I want to check these boxes? Do I need to include these options in the preprocessing pipeline if I select 'T1 Dicom to Nifti' as well? Also, if I check one of the interactive reorientation options (e.g. 'ReorientT1*'), do I then also have to select the others (e.g. 'Reorient Fun*' and 'Reorient after Coregistration*')?
  3. Can you please tell me what would be the parallel (equivalent) functions for the DPARSFA 'Reorient Fun*', 'Reorient T1*' and 'Reorient after Coregistration*' options in SPM? 

Thank you very much in advance. As always, your advice would be much appreciated and has so far helped me a great deal with my pre-processing and statistical analysis. I am finding it relatively easy to work with the DPARSFA toolbox, but want to make sure that I understand what the different pre-processing steps involve.

Kind regards,
Mamtis


Submitted by ZHANG_RESTadmin on Tue, 12/03/2013 - 00:12

 1. Yes the two steps you mentioned are performed. Reorientation I don't know (you can refer to MRIcroN website for help), crop is to remove the neck.
 2. Yes you are correct they are for interactive, manual reorientation. When your functional image is not in good position and thus you have trouble to achieve coregistration between functional image and structure image, you should check reorient fun and reortient T1 both, and un-check the third interactive option.    When you don't have those problems (this will be the most cases), just check the third option (in this case you don;t have to check the first two options.)
 3. The similar funciton in SPM is not obvious, you can see SPM manual for Display --> reorientation