Hi Matt, thanks. I made an error previously and it worked now. With the
command lines you wrote, I noticed there isn't a need for the TE of the
EPI, whereas this parameter is required in the FEAT GUI prestats B0
unwarping. Why is that so?
Thanks
Siewmin
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
>
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