Dear Alfonso,
Thank you for your help and explanation.
My goal is to obtain REX ROI activity extractions for atlas ROIs, but to not draw on voxels activity from outside of the field of view (because of course those voxels would not be valid). See top left image in the attached for a group-level mask I made from threshold the wau* files (these data will not be smoothed). These are voxels that the group have in common and show the limited FOV.
I have been thinking of several ways to try to accomplish my goal. 1) Enter this group mask back into Setup.options in place of the default Analysis mask (mask.volume) to restrict all analyses to the voxels in the FoV or 2) As you suggested, change the Setup.ROI Grey Matter ROIs to the functional gray matter files (which are the wc1art_mean_au*.nii files?) and then pressing DONE and re-running the de-noising stage. Does either approach work?
Finally, in a first pass of this analysis, errors would be thrown for ROI #59 for REX extraction step that "warning: no valid data for" ROI #59, yet in the ROI resulting files in the data structure there were still TR-wise numbers for those ROIs. Is the data were not valid, what is being reported there? Should those numbers be NaNs? it was correct for ROI #59 to throw an error because it is the precentral gyrus and is outside of the FOV, but there are others that also should have had this error.
Thank you!
Sarah Kark
Thank you for your help and explanation.
My goal is to obtain REX ROI activity extractions for atlas ROIs, but to not draw on voxels activity from outside of the field of view (because of course those voxels would not be valid). See top left image in the attached for a group-level mask I made from threshold the wau* files (these data will not be smoothed). These are voxels that the group have in common and show the limited FOV.
I have been thinking of several ways to try to accomplish my goal. 1) Enter this group mask back into Setup.options in place of the default Analysis mask (mask.volume) to restrict all analyses to the voxels in the FoV or 2) As you suggested, change the Setup.ROI Grey Matter ROIs to the functional gray matter files (which are the wc1art_mean_au*.nii files?) and then pressing DONE and re-running the de-noising stage. Does either approach work?
Finally, in a first pass of this analysis, errors would be thrown for ROI #59 for REX extraction step that "warning: no valid data for" ROI #59, yet in the ROI resulting files in the data structure there were still TR-wise numbers for those ROIs. Is the data were not valid, what is being reported there? Should those numbers be NaNs? it was correct for ROI #59 to throw an error because it is the precentral gyrus and is outside of the FOV, but there are others that also should have had this error.
Thank you!
Sarah Kark