Hi Xiaomin, I finally got around to looking at this, and this is a bug. The "cespct" is not actually a percent, rather it is a fraction of the mean functional. However, the "cesvarpct" is a percent, which makes the group ffx analysis with percent fail. I have fixed this in both dev and stable such that cespct is actually a percent, live on next update. Let me know if this does not fix your problem.
doug
xiaomin wrote:
Hi,
I am running the following command for group fixed factor and random factor analysis with and without percent parameter on.
Here are the commands:
- for the no percent:
isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -hemis -o . -subject fsaverage mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh
- for the percent:
isxconcat-sess -sf subjlist -df subjdir -analysis RotDepth -all-contrats -percent -hemis -o . -subject fsaverage mri_glmfit --y rh.cespct.nii --osgm --glmdir pct.rh.ffx.osgm --nii --mask ../rh.mash.nii --yffxvar rh.cesvarpct.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh
However, the significance between percent and no percent is inconsistent. For testing if the data has problem, I run it with rfx design. The significance between percent and no percent is almost same. (see attached graph) Second, the significance with percent parameter for the fixed factor analysis is very small, which is abnormal. We need to use ffx significant map to define a ROI.
The data is here:
/autofs/space/yneuron_001/users/xiaomin/projects/FaceRotation/subjects/Rot_D epth.
Xiaomin Yue Research Fellow NMR center, MGH
