 |
 |
I would try converting the field maps using dcm2nii, in the MRIcron package, or MRIConvert and see if you get the correct intensities that way (I use dcm2nii and get intensities that work). As for trying to manually scale the images, I am honestly not sure, perhaps someone else on the list knows better. About the IPAT, I think that is correct, but again someone else on the list should verify as that is the kind of question I would tend to ask one of my BME colleagues with more extensive MR physics background. ;) Regarding the "few voxels more" could you send me a screenshot of what you are talking about? Were your brain extractions good? You might need to modify the bet lines in the code I sent to be optimal for your data (specifically the -f option, and -g might need to be set as well). Peace, Matt. -----Original Message----- From: Siewmin Gan [mailto:[log in to unmask]] Sent: Friday, May 01, 2009 12:17 PM To: [log in to unmask]; Matt Glasser Cc: Siewmin Gan Subject: Re: problem running FEAT 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