help > overlay stat map
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Oct 12, 2017  03:10 PM | Sebastian Rodrigo - Paris-Descartes University
overlay stat map
Dear Surf Ice guru,

I try to overlay some fMRI Zstat map generated by Feat (FSL). Surf Ice could load a map on surface only from the FSL stat folder (such as zstat1.nii.gz for example) and failed with thresh_zstat1.nii.gz at the root of the Feat analysis folder. Surf Ice said "Error: no variability in overlay 0".
May be It could be related to the NIFTI field CAL_MAX & CAL_MIN. Those two fields are set to 0 in thresh_zstat1.nii.gz and seemingly correct values in zstat1.nii.gz. Are CAL_MAX & CAL_MIN fileds related to message error fo Surf Ice ? How can I corectly set those fields ? I could found a way to set it  with fsl tools to modify nifti header or create nifti header. I need to manipulate thresh_zstat1.nii.gz to apply registration matrix to the volume used to generate the surface file.

Best regards

Sebastian
Oct 14, 2019  07:10 AM | Chris Rorden
RE: overlay stat map
Sorry for the late reply, I missed this message. I suspect the issue is that your statistical map is not in the same space as the mesh you are attempting to overlay the data onto. For the first level analyses, the statistical map thresh_zstat1.nii.gz will be in the native space of your scanner (e.g. the origin is isocenter of the magnetic field, spatial directions are with respect to scanner bore), not in any standard space (origin is anterior commissure, space is with respect to template). You would either want to make a participant specific brain mesh, or you will want to warp your statistical map into standard space. Without this step, the statistical map will not be in register with your mesh. The simplest fsl command for this (assuming on linear warping) would be:


flirt -ref reg/standard -in thresh_zstat1 -applyxfm -init reg/example_func2standard.mat -out thresh_zstat1_2standard