I am investigating dynamic brain connectivity of resting state fMRI data. I have done different steps of preprocessing including: those mentioned in "Ashkan Faghiri et al., 2018", registeration into MNI space and interpolation of the voxel size to 333 iso. At the same time, anatomical data have brain extracted and registered to MNI space. Using FSL FAST, anatomical masks of CSF, WM and GM for each subject has created. Finally, spatial group ICA has applied on functional data using GIFT.
The main question I could not exactly find an answer to it through GIFT manual or Walk through is : whether I am able to use "spatial sorting tool in Display GUI" to find noise components indicating activation in WM and CSF using created masks by FSL FAST or not?
If yes,
1. Should the process be run separately for each subject or is it enough to find noise components (associated with WM and CSF) for a subject and then omit those components for other subjects in advance (according to the spatial group ICA characteristics)?
2. How should I choose the mask for “Load Anatomical” section? Should I just use one of the subjects’ brain extracted anatomical image or leave it with the default setting (first image of the functional data)?
3. In the next stage, which Spatial Sorting Criteria (Maximum Voxel or Correlation) should be selected?
4. Should I choose one of the subjects’ CSF or WM mask for the Spatial Template?
5. In the end, what threshold should be considered to identify components associated with the mask??
Sorry for the long question.
Any guidance and clarification would be fully appreciated.
Merry Christmas,
Ali
Last edit: Mohammadali Javanray 2018-12-28
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Dear GIFT experts,
I am investigating dynamic brain connectivity of resting state fMRI data. I have done different steps of preprocessing including: those mentioned in "Ashkan Faghiri et al., 2018", registeration into MNI space and interpolation of the voxel size to 333 iso. At the same time, anatomical data have brain extracted and registered to MNI space. Using FSL FAST, anatomical masks of CSF, WM and GM for each subject has created. Finally, spatial group ICA has applied on functional data using GIFT.
The main question I could not exactly find an answer to it through GIFT manual or Walk through is : whether I am able to use "spatial sorting tool in Display GUI" to find noise components indicating activation in WM and CSF using created masks by FSL FAST or not?
If yes,
1. Should the process be run separately for each subject or is it enough to find noise components (associated with WM and CSF) for a subject and then omit those components for other subjects in advance (according to the spatial group ICA characteristics)?
2. How should I choose the mask for “Load Anatomical” section? Should I just use one of the subjects’ brain extracted anatomical image or leave it with the default setting (first image of the functional data)?
3. In the next stage, which Spatial Sorting Criteria (Maximum Voxel or Correlation) should be selected?
4. Should I choose one of the subjects’ CSF or WM mask for the Spatial Template?
5. In the end, what threshold should be considered to identify components associated with the mask??
Sorry for the long question.
Any guidance and clarification would be fully appreciated.
Merry Christmas,
Ali
Last edit: Mohammadali Javanray 2018-12-28