Hi Souheil, does NIFTI store the MR parameters?
thanks Bruce On Tue, 28 Aug 2012, Inati, Souheil (NIH/NIMH) [E] wrote: > On most (all?) scanners TR is stored as an integer. For example, on siemens it's in microseconds and then stored as a long. (this is the value in the protocol, not the actual execution TR, but when/if there are no bugs, then this is correct). When you convert a long to float (single or double precision) you will get some junk in the low bits because of type conversion. In the dicom it's all string representations. > > Does the dicom say 50.000 or 50? > How does the conversion from int > > -- > > Souheil Inati, PhD > Staff Scientist > Functional MRI Facility > NIMH/NIH/DHHS > souheil.in...@nih.gov > > > > > On Aug 28, 2012, at 12:06 PM, Bruce Fischl wrote: > >> does NIFTI support the MR parameters? I'm not sure it does. I suspect >> that 50 is correct and not 50.000000745058060 (can you imagine setting >> that on the console)? >> On Tue, 28 Aug 2012, dgw wrote: >> >>> Hi, >>> >>> I'm not sure if this is a bug report or a feature request. I have been >>> using mri_convert to convert dicoms to nii.gz and mgz files, and I >>> have noticed some discrepancies when reading the volumes in with >>> MRIread in either matlab or octave. The volumes differ in their >>> support of the flip angle, tr, te, and ti fields (I realize some of >>> this may be due to file type differences). Thought the standard output >>> of mri_convert shows the expected values. >>> >>> In the mgz file the TR seems to be rounded i.e. >>> 50 instead of 50.000000745058060 in the nii.gz >>> >>> In the mgz file the flip angle and te are recorded >>> FA 0.52.... while in the nii.gz it is 0 >>> te 10.39... while in the nii.gz it is 0 >>> >>> The ti value appears strange to me in the mgz >>> ti = -1 while in the nii.gz it is 0 >>> >>> I have generated two files using mri convert off of the same MR volume >>> as a test case: >>> /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/877000-000020-000003.dcm >>> >>> /cluster/hbot/agario_p2_2/dcm/020_t1_fl2d_tra_TEMP/004/volume.nii.gz >>> >>> /cluster/hbot/agario_p2_2/dcm/test.mgz >>> >>> These files were generated using /usr/local/freesurfer/stable5_1_0/ >>> >>> Thanks, >>> D >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
