Hi,
I think this is quite a basic question but I do need some comments to clarify my concept.
I have performed 1st-level analysis and produced feat directory for each of my subject's fmri data. In registration process, linear registration was used from fmri to main structural image, and nonlinear was selected in standard space registration. Files in reg are listed at the bottom.
I selected a mask from Juelich atlas in FSL (called mask.nii.gz), which is in standard space. I want to get the statistics in this mask in COPE1 (such as signal change) of individual subject (feat directory) using featquery.
Now I'm in the 1st-level feat directory of subject s01, which contains several COPEs. I used the command line below:
featquery 1 s01.feat 1 thresh_zstat1 output_name -a 3 -p -s -w -b mask.nii.gz
Am I correct?
My concern is, should I transform the space of the mask to individual space by applywarp? If the answer is yes, is the command below performed in reg directory correct?
applywarp -i mask.nii.gz -o output_name -r example_func -w standard2example_func.mat
I don't know which one in reg directory (from the "Files in reg directory" listed below) should be selected for -w. Any comment is appreciated and thanks in advance.
Best,
Mark
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Files in reg directory:
example_func.nii.gz
example_func2highres_1vol.nii.gz
example_func2highres_fast_wmedge.nii.gz
example_func2highres_fieldmap2str_init.mat
example_func2highres_fieldmaprads2epi.nii.gz
example_func2highres_fieldmaprads2str_dilated.nii.gz
example_func2highres_fieldmaprads2str_pad0.nii.gz
example_func2highres_fieldmaprads2str.nii.gz
example_func2highres_init.mat
example_func2highres_inv.mat
example_func2highres_warp.nii.gz
example_func2highres.mat
example_func2highres.nii.gz
example_func2highres.png
example_func2standard_warp.nii.gz
example_func2standard.mat
example_func2standard.nii.gz
example_func2standard.png
example_func2standard1.png
highres_head_to_standard_head.log
highres_head.nii.gz
highres.nii.gz
highres2example_func.mat
highres2highres_jac.nii.gz
highres2standard_linear.nii.gz
highres2standard_warp.nii.gz
highres2standard_warp_inv.nii.gz
highres2standard.mat
highres2standard.nii.gz
highres2standard.png
standard_head.nii.gz
standard_mask.nii.gz
standard.nii.gz
standard2example_func.mat
standard2highres.mat
unwarp
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