open-discussion > About mICA can not choose mask
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Jul 23, 2017  08:07 PM | liu lin
About mICA can not choose mask
Dear all,

 when I choose

1)    the Multi-session(group)ICA in 'Perform'
2)    input 122 4D nifti files

however, here I can not choose the mask, only custom mask can be chose.

I want to choose the MNI Structural Atlas Cerebellum, how should I do?

thanks a lot

yours

lin
Jul 25, 2017  01:07 AM | Jorge Manuel S├ínchez - Hannover Medical School
RE: About mICA can not choose mask
Dear Lin,

I would suggest to check two things.
  • The mICA Toolbox looks for the atlases in the directory ${FSLDIR}/data/atlases. Could you check if your atlas directory is there?
  • The toolbox also checks, whether the matrix size and the orientation of the nifti files correspond to the MNI-space. The matrix size should be either 91x109x91 or 182x218x182 or 364x436x364; and the qform_name should be MNI_152 (qform_code 4). If this is not the case, the mICA Toolbox will only allow to choose custom masks.

Kind regards,

Jorge
Jul 26, 2017  12:07 AM | Florian Beissner
RE: About mICA can not choose mask
Dear Lin,
in general you have to make sure that your input data are already normalized to the template that your mask(s) come from. That means if you want to use an MNI space based atlas, your data need to be normalized to MNI space. Please not that there are differences in MNI templates between FSL and SPM. Our toolbox is based on FSL. As Jorge has pointed out, mICA will check the bounding box of your input data and only allow MNI-based atlases if it matches that of the template. In every other case, it will only allow custom masks.

Hope that helps,

Florian
Jul 28, 2017  03:07 AM | liu lin
RE: About mICA can not choose mask
Dear Jorge,

Thank you so very much. Now, my data set [1] 122 participants(83patients & 39healthy) [2] preprocessing have been done using FSL MELODIC (I have been completed the ICA and dual regression) .

My question: 

1) If I want to know the relationship between the brain stem and other whole brain regions using mICA, how should I do?
2) In the paper 'MICA-A toolbox for masked independent component analysis of fMRI data'  Fig. 4 (a)(b), is this necessary for me to decide the number of component? 
does this figure mean that if I donot sure the number of component I can use the 'mICA reproducibility analysis'?

thanks a lot 
Kind regards,

lin
Jul 28, 2017  03:07 AM | liu lin
RE: About mICA can not choose mask
Dear Florian,

Thank you so very much. Now, my data set [1] 122 participants(83patients & 39healthy) [2] preprocessing have been done using FSL MELODIC (I have been completed the ICA and dual regression) .
My question:
1) If I want to know the relationship between the brain stem and other whole brain regions using mICA, how should I do?
2) In your research 'MICA-A toolbox for masked independent component analysis of fMRI data' Fig. 4 (a)(b), is this necessary for me to decide the number of component?
does this figure mean that if I donot sure the number of component I can use the 'mICA reproducibility analysis'?

thanks a lot
Kind regards,


lin