Applying and Inverting Transformations [on mask]

笛里谁知壮士心,沙头空照征人骨。这篇文章主要讲述Applying and Inverting Transformations [on mask]相关的知识,希望能为你提供帮助。
cr:  http://fsl.fmrib.ox.ac.uk/fslcourse/2019_Beijing/lectures/Registration/FSL_Registration_Practical.pdf
the story starts from a question...

If we were interested in the functional signal in (for example) the amygdala within the fMRI data in a particular subject, which space would we transform a standard mask of the amygdala into for further processing?
  • The structural space - we want to make sure we get the most accurate signal from the data, and this is when the image is in structural space
  • The distortion-corrected functional space - we do our task analysis in functional space, once it has been corrected for distortions
  • The native functional space - we do our task analysis in functional space, without any registrations applied
the correct answer is no.2. but how come?
 
0.1. get familiar with transformation files
  • highres2standard.mat
  • highres2standard_warp.nii.gz
  • ...
0.2  three main spaces in a FEAT analysis
  • functional (represented by  example_func);
  • structural (represented by  highres);
  • MNI (represented by  standard)
 
 
1.  Creating an example mask [in MNI space] [from existing Atlases]
fsleyes -std &

......gui acts
2.  Inverting a transform [to get std2highres_warp)
invwarp -w highres2standard_warp -o standard2highres_warp -r highres

Applying and Inverting Transformations [on mask]

文章图片

3.  Applying a transformation
applywarp -i LeftHippMask -r example_func -o LeftHippMaskFunc -w standard2highres_warp --postmat=highres2example_func.mat

Applying and Inverting Transformations [on mask]

文章图片

 
4.  Thresholding the Mask [now in func space] [to make it binary]
4.1 to choose 1)0.9, tighter; 2)0.5, of similar size/volume as before; 3)0.1, ok to include neighbouring stuctures.
4.2 
fslmaths LeftHippMaskFunc -thr 0.9 -bin LeftHippMaskFuncBin

5.  Using the Mask
e.g. 
fslmeants -i ../filtered_func_data -m LeftHippMaskFuncBin

【Q】why  filtered_func_data, the  pre-processed fMRI data
 
【Applying and Inverting Transformations [on mask]】 

    推荐阅读