Hi,
> Hello Mark,
>
> I have a few questions about this practical. Could you please clarify?
>
> 1. Under "Processing the fieldmap phase difference image": "Here we need to take this raw scanner output, which is scaled in a strange way (0 to 360 degrees are mapped to 0 to 4096), and convert it into a radians per second image." Why do we have to do this?
Because the tools need values with particular units.
> 2. Just before "Using the FEAT GUI": "View the output with fslview and check that most of the brain has small values (less than 100) while in the..." What is the point here?
To familiarise yourself with the data.
> 3. Last paragraph of "Using the FEAT GUI". I followed the steps and tried six times. Whenever I pressed the "Go" button, I got the following error:
>
> ERROR: you haven't filled in all the relevant selections with valid filenames:
> Problem with FEAT input file (1): currently set to "/home/fslcourse/fsl_course_data/reg/feat_example/func_data"
If you have installed your data in a location that is different to /home/fslcourse/fsl_course_data, then you need to change this input file location.
> 4. Under "Registration command (FNIRT)" - "Visual Check (images)": The image created using FNIRT seems to match the MNI152_T1_2mm better than that created using FLIRT because of non-linearity. Is this the point you are trying to make?
Yes.
> 5. Under "Applying and Inverting Transformations"' - "Visual Check": Again, the image created using FNIRT seems to match the MNI152_T1_1mm better than that created using FLIRT because of non-linearity. Is this the point you are trying to make?
Yes.
> What is the different between this and the previous comparison mentioned in Point 4? What is the point of using high-res?
In some situations you will want to move things between different spaces.
> 6. "Standard-space masking - a useful application". Could you please explain what "standard-space mask" and "individual functional image" are?
"standard-space mask" is a mask image in the standard space.
"individual functional image" is one image from a functional series.
> 7. "Fine Adjustments using Initialisation" - "Visual Check". Compared with the previous translation-only result, it seems that there is NO improvement using fine adjustment because I see the images being cut into two pieces and joined together like a step. Is this the "tilted" arbitrary cutoff line you mentioned in next paragraph?
Yes.
> 8. The paragraph before "Getting to Know the Transformation Matrix (Optional): "Note that a small FOV image that is "tilted".." I don't quite understand what you are talking about here. Could you please clarify?
I don't really know what you are asking here. The sentence about tilting was referring to the "cut" that you see in individual slices.
All the best,
Mark
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