Hi - yes it may depend on the context/pipeline but for simplicity and safety pretty much everything we do just works in floats. Cheers
> On 3 Mar 2016, at 21:18, Harms, Michael <mha...@wustl.edu> wrote: > > > Maybe Steve or MJ can chime in regarding the FSL issues, but I do recall > there being some concern years ago whether ‘FSL’ was fully compliant with > UINT16 NIFTI’s. > > Regardless, in terms of what we are currently using, it is FLOAT32. > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson > <tsc...@mst.edu <mailto:tsc...@mst.edu>> > Date: Thursday, March 3, 2016 at 3:14 PM > To: "Garrett T. McGrath" <gmcgr...@princeton.edu > <mailto:gmcgr...@princeton.edu>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Negative Voxel Values signed int 16 vs uint16 issue > > NiFTI-1.1 does in fact support both signed and unsigned int16: > > #define DT_INT16 4 > ... > #define DT_UINT16 512 /* unsigned short (16 bits) */ > > I don't know if this was the case in NiFTI-1.0, but NiFTI-1.1 has been around > so long it would be strange if tools didn't support it, but did support 1.0. > If dcm2nii or MRICron is treating them incorrectly, then you should contact > the tool's authors. MRICron isn't reading it as analyze format, is it? The > old analyze format doesn't support uint16. > > I don't know whether topup cares what the input datatype is. float32 can > exactly represent any value of int16 or uint16, so it seems unlikely that > conversion to float32 would cause problems (unless the data scaling and > offset do something unusual...). > > Tim > > > On Thu, Mar 3, 2016 at 2:42 PM, Garrett T. McGrath <gmcgr...@princeton.edu > <mailto:gmcgr...@princeton.edu>> wrote: >> We've had a set of users that have discovered an issue with their latest >> datasets that I'm hoping there might be a best practice for dealing with in >> regards to FSL. >> >> I've received some specific context from the end users on what they are >> capturing: >> Users are collecting single-band spin echo EPI images in opposing phase >> encode directions with the CMRR sequence (cmrr_mbep2d_se) on our 3T Prisma >> to provide means of correcting for susceptibility distortions via FSL’s >> ‘TOPUP’ tool. Their protocol parameters closely follow what is specified in >> the HCP Q3 Release Appendix I. The dicom output of this data is UINT16 which >> isn’t supported by nifti 1.0 format. Is there a recommended solution that >> would play nice with FSL (TOPUP in particular) ? With the dcm2nii conversion >> tool, we can either go ahead and set the data type to UINT16 or set it to >> float32, but is there a specific recommendation from your end? >> >> I've verified the values using the MRICron tool to visually inspect values >> and they are infact overflowing into negative numbers so we have a few >> options: Force unit16 (out of standard), force Float32 (in standard but >> larger, slower, and brings along the baggage of float numbers), divide all >> intensities by 2 (lossy, I don't regard it as an acceptable solution for raw >> data), or fall back on dicom files (I'm not clear if this is supported by >> FSL). >> >> Any suggestions or feedback would be appreciated. >> >> Garrett McGrath >> HPC and Research Computing >> Princeton Neuroscience Institute, Princeton University >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
