I don't think your DICOM to NIFTI conversion program is working correctly as
some of those images have way too many slices in the z direction. Perhaps
you can look at those DICOM files with a DICOM viewer like
http://nrg.wustl.edu/projects/DICOM/DicomBrowser.jsp and you can see what
that says you have. Perhaps you have just a single field map (there are a
variety possibilities here, could be up to 4 volumes) and an EPI sequence
(or several of them).
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Jenifer Juranek
Sent: Tuesday, September 28, 2010 4:43 PM
To: [log in to unmask]
Subject: Re: [FSL] field map for Philips 3T
Thanks, Matt.
Your comments on what I do have (see fslinfo below) would be very helpful
(since I'm not sure what I need vs what I received). I've looked at the
following for some guidance, but the data I received does not seem to fit.
http://www.fmrib.ox.ac.uk/fsl/fugue/feat_fieldmap.html
Any ideas what I have here?
1) 2040 dicom files
2) dcm2nii -->16 phase and magnitude image pairs
3) 2 unpaired image files (see fslinfo below)
4) partial FOV (inferior portion of the brain only...mainly subcallosal
along the entire A-P axis...z=31 in each pair)
magnitude image (#7 out of 16)
fslinfo 20100914_153118IM_0007B0mapSENSEPPSF002s801a6008A.nii
data_type INT16
dim1 256
dim2 256
dim3 32
dim4 2
datatype 4
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 2.0000000000
pixdim4 0.0500000007
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
phase image (#7 out of 16)
fslinfo 20100914_153118IM_0007B0mapSENSEPPSF002s801a6008.nii
data_type INT16
dim1 256
dim2 256
dim3 56
dim4 1
datatype 4
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 2.0000000000
pixdim4 0.0500000007
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
Unpaired image file with combination of phase info (in X,Y planes of FSLview
window) and a magnitude image (whole brain) in the Z plane FSLview window
fslinfo 20100914_153118IM_0017B0mapSENSEPPSF002s801a008.nii
data_type INT16
dim1 256
dim2 256
dim3 1087
dim4 1
datatype 4
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 2.0000000000
pixdim4 0.0500000007
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
Unpaired image file all 3 planes of FSLview window contain complex data
fslinfo 20100914_153118IM_0001B0mapSENSEPPSF002s801a008.nii
data_type INT16
dim1 256
dim2 256
dim3 953
dim4 1
datatype 4
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 2.0000000000
pixdim4 0.0500000007
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
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