Hi folks, We're altering some of our HCP scripts to use updated T1w and T2w in a new project and I want to make sure I'm entering the correct "Sample Spacing" values for TOPUP distortion correction in the PreFreeSurferPipelineBatch.sh step. Tim's annotation of the PreFreeSurfer.sh code refers to DICOM field 0019,1018 for Siemens. In our Skyra T1w data, this field contains a rather unhelpful "6500" value, which is nothing like the sample values.
There's also annotation in the PreFreeSurferPipelineBatch.sh script for GE scanner users, which refers to 1/((0018,0095)x(0028,0010)). Although we don't have a GE scanner, these fields give us information that creates a value comparable to the example given (e.g., for the T1 these fields refer to ACQ Pixel Bandwidth=240 and IMG rows=320... the resulting value is feasible = .00001302083333). The only other thing I have available is an "echo spacing" value from our T1w scan sequence card. This is originally what I thought was correct given how this is the term used when describing the unwarping of fMRI images and used for the fieldmaps themselves. However, that T1w echo spacing value of 7.6 msec is used (even when specified in sec, e.g., .0076), the resulting T1w_acpc_dc_brain.nii.gz image is wildly distorted (and I don't think it's because I'm using the wrong phase encoding value... It's equally weird whatever phase encoding value I try). If anyone can clarify were exactly we can find the sample spacing info that should be used with the HCP scripts, I'd appreciate it. Best, Mike Michael C. Stevens, Ph.D. Director, Clinical Neuroscience & Development Laboratory, Olin Neuropsychiatry Research Center Director, Child & Adolescent Research, The Institute of Living / Hartford Hospital Adjunct Associate Professor of Psychiatry, Yale University School of Medicine This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
