Hi Matt, thank you very much for your help.
Can I ask you a basic question?
I assume the 2 GRE maps I have are a realfieldmap and a magnitude map from
comparing them to the fsl webpage on how they may look like. The "realfieldmap" dicom
has intensity -4096 to + 4094. Am I right to then prepare this realfieldmap by calculating
it to make it of a range from either -pie to pie or 0 to 2 pie?
With the fieldmaps, they are acquired from a 3T Siemens Scanner and converted from
dicom to Analyze/Nifti using Debabeler. I also tried another way to convert them, this
time using SPM. The fieldmap output from SPM would retain intensity values from -4096
to +4092. I tried to multiply them by 3.14 and divide by 4096 and their intensity range
becomes-pie to pie or -3.14 to + 3.14. However, when I input this into the Feat Gui, an
error msg pops up with "Error:Child Process Exited Abnormally". May I ask what may be
the reason for this? I read there is no difference between the two ranges but the former
range fieldmap I have doesn't seem to be accepted on the GUI. Would it matter if the
intensity are from -pie to pie using the command lines?
I tried the command lines you've written. I noticed a few voxels more in the brain edges
in the output undistorted images compared to the original 4D data. I'm not sure if it's due
to masking. I tried both y and y- directions and there is no difference in the output. If this
is so, could this mean that my input data is faulty, so the output from the command lines
didn't undistort the data? Also, with the command lines, if I use IPAT 2 parallel processing
on the Scanner, should I input 1/2 the dwell time when running this function?
I tried the FSL FEAT GUI again now, and there are more command lines coming out of the
log file. I'm waiting to see if I could get output files this time. For using the GUI to only
do B0 distortion, is it necessary to apply spatial smoothing FWHM and /or Temporal
Filtering option on the pre-stats section?
Many Thanks again.
Siewmin
|