Hi, We’ve been going with FLOAT32 in our conversions, which I believe is the default behavior of ‘dcm2nii’.
cheers, -MH -- 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 63110Email: [email protected] On 3/3/16, 2:42 PM, "[email protected] on behalf of Garrett T. McGrath" <[email protected] on behalf of [email protected]> 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 [email protected] 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
