Hi everyone,
I must apologize ahead of time for the novice questions I am about to ask.
1) Unique missing-mask voxels:
(I've uploaded a word doc with screen shots of the results I got from my
gfeat analysis: http://drop.io/linspace/media )
-From this picture, how would I go about figuring out who it is that's
missing those voxels?
-If this is a registration problem, how would I fix it?
-Any general comments or suggestions from looking at my results?
2) (First Level Analysis) Threshold activation images:
I've noticed that the threshold end points varied between subjects. Why is
this the case? For example one subject's threshold is 2.3-9 while another
went from 2.3-11.8. I left the Z threshold at the default value for all of them.
3) Registration report:
-What is the difference between FMRI and example_func in the registration
report?
-What is the difference between standard space and standard in the
registration report?
4) ROI analysis
I have a set of localizer scans in which I hope to define the FFA and use
that to analyze my experimental fmri's. I have several points of confusion:
- I've tried fslroi and fslmaths and the result was blank, yet still showed
activation in the timeseries plots in fslview. After looking through the
forums I realized that in coordinates for these fslutils require voxel space
coordinates. I am looking for the highest activating voxel within 30<x<50,
-60<y<-30, -30<z<-5 (Talairach coordinates) and I am defining the ROI as the
area 8mm from that point (in all directions). Once I convert to MNI (FSL's
coordinate system, if I'm not mistaken), how would I go from MNI to voxels?
If I had to draw the ROI in fslview how would I determine the highest
activating voxel there? (I'm still a bit confused about what the different
sets of coordinates in the cluster browser are).
- While playing around with fslroi and fslmaths, I became increasingly
confused about whether I should be extracting from my 4D fMRI image or the
thresh_zstat image.
- When would one use featquery? How would one choose which mask to use?
Would this be the mask I drew in fslview?
-Has anyone had experience with fslroi toolbox? This seems relevant to what
I am trying to do but I'm not quite sure how to use it. Is it run from the
unix command line or does this need to be linked to matlab somehow?
Again, I'm very sorry for the bombardment of novice questions; I'm
relatively new to FSL and fMRI analysis. Any help would help me out a lot.
Thank you all so much for all your help.
Lin Nga
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